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 BS_biosap_search 1 biosap_search_id BIOSAP Search ID int 4 0 N Y Y N N Y pkDEFAULT BS_biosap_search 2 biosap_search_idcode BIOSAP Search ID Code varchar 255 0 Y N N N N N BS_biosap_search 3 search_username Search Username varchar 255 0 Y N Y N N N Name of User BS_biosap_search 4 search_date Search Date datetime 8 0 N CURRENT_TIMESTAMP N Y N N N Date on which search was performed BS_biosap_search 5 biosap_version BIOSAP Version varchar 255 0 Y N N N N N Version of BIOSAP used BS_biosap_search 6 biosap_desc Description varchar 255 0 N N N N N N BIOSAP Description BS_biosap_search 7 organism_id Organism ID int 4 0 N N organism organism_id N optionlist 5 Y Y N Organism on which BIOSAP is being used SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name BS_biosap_search 8 comments Comments varchar 255 0 Y N N textarea 5 Y Y N Comments for this BIOSAP run BS_biosap_search 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N BS_biosap_search 10 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N N BS_biosap_search 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N BS_biosap_search 12 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N N BS_biosap_search 13 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N N BS_biosap_search 14 record_status Record Status char 1 0 N N N N N N BS_featurama_parameter 1 biosap_search_id BIOSAP Search ID int 4 0 N Y Y N N Y pkDEFAULT BS_featurama_parameter 2 gene_library Gene Library varchar 255 0 N N Y Y Y N Library of Biosequences used in the BIOSAP search BS_featurama_parameter 3 melting_temp Melting Temperature real 4 0 N N Y Y Y N Temperature at which 50% of the oligonucleotides exist in the denatured form BS_featurama_parameter 4 melting_temp_range Melting Temperature Range real 4 0 N N Y Y Y N Degrees to which the melting temperature can fluctuate when determining acceptabl oligonucleotides BS_featurama_parameter 5 minimum_length Minimum Length int 4 0 N N Y Y Y N Minimum length of oligonucleotide reporter BS_featurama_parameter 6 maximum_length Maximum Length int 4 0 N N Y Y Y N Maximum length of oligonucleotide reporter BS_featurama_parameter 7 maximum_selfcomp Maximum Self Comp. Score int 4 0 Y N Y Y Y N Maximum self-complementarity score BS_featurama_parameter 8 step_size Step Size int 4 0 N N Y Y Y N Number of nucleotides the selection window will shift during oligonucleotide selection BS_featurama_parameter 9 maximum_3prime_distance Maximum 3 Prime Distance int 4 0 N N Y Y Y N Maximum distance from the 3 prime end for selecting oligonucleotides BS_featurama_parameter 10 initial_3prime_offset Initial 3 Prime Offset int 4 0 Y N Y Y Y N Beginning distance from the 3 prime end for selecting oligonucleotides BS_featurama_parameter 11 maximum_features Maximum Features int 4 0 N N Y Y Y N Maximum number of reporters to be found per biosequence BS_featurama_parameter 12 maximum_polyAT_length Maximum Poly AT Length int 4 0 N N Y Y Y N Maximum length of consecutive A/T base pairs BS_featurama_parameter 13 maximum_polyGC_length Maximum Poly GC Length int 4 0 N N Y Y Y N Maximum length of consecutive G/C base pairs BS_featurama_parameter 14 content_window_size Content Window Size int 4 0 N N Y Y Y N Window size for heuristic tests BS_featurama_parameter 15 maximum_windowAT_content Maximum Window AT Content int 4 0 N N Y Y Y N Maximum number of A/T base pairs in the content window BS_featurama_parameter 16 maximum_windowGC_content Maximum Window GC Content int 4 0 N N Y Y Y N Maximum number of G/C base pairs in the content window BS_featurama_parameter 17 oligo_concentration_mMol Oligo Concentration mMol real 4 0 N N Y Y Y N Oligonucleotide Concentration in mMol BS_featurama_parameter 18 salt_concentration_mMol Salt Concentration mMol real 4 0 N N Y Y Y N Salt Concentration in mMol BS_featurama_statistic 1 biosap_search_id BIOSAP Search ID int 4 0 N Y N N Y pkDEFAULT BS_featurama_statistic 2 n_features_found Number of Features Found int 4 0 N N Y Y N Number of reporters found BS_featurama_statistic 3 n_featureless_genes Number of Featureless Genes int 4 0 Y N Y Y N Number of biosequences for which no reporters were found BS_featurama_statistic 4 gene_rep_fraction Gene Represented Fraction real 4 0 Y N Y Y N Fraction of biosequences for which a reporter was found BS_featurama_statistic 5 success_fraction Success Fraction real 4 0 Y N Y Y N BS_featurama_statistic 6 self_comp_features_rej Rejected Features- Self Comp. int 4 0 Y N Y Y N Number of reporters rejected due to self-complementarity criteria BS_featurama_statistic 7 high_Tm_features_rej Rejected Features- High Tm int 4 0 Y N Y Y N Number of reporters rejected due to high melting temperature BS_featurama_statistic 8 low_Tm_features_rej Rejected Features- Low Tm int 4 0 Y N Y Y N Number of reporters rejected due to low melting temperature BS_featurama_statistic 9 content_features_rej Rejected Features- Content int 4 0 Y N Y Y N Number of reporters rejected due to heuristic criteria BS_featurama_statistic 10 duplicate_features Duplicate Features int 4 0 Y N Y Y N Number of duplicate reporters found BS_featurama_statistic 11 n_features_considered Number of Features Considered int 4 0 Y N Y Y N Number of reporters considered BS_featurama_statistic 12 featurama_version Featurama Version varchar 50 0 Y N N N N Version of Featurama BS_feature 1 feature_id Feature ID int 4 0 N Y N N Y pkDEFAULT BS_feature 2 biosap_search_id BIOSAP Search ID int 4 0 N N N N N BS_feature 3 biosequence_id Biosequence ID int 4 0 N N biosequence biosequence_id N N N BS_feature 4 melting_temp Melting Temperature real 4 0 Y N Y Y N Temperature at which 50% of the oligonucleotides exist in the denatured form BS_feature 5 threeprime_distance Three Prime Distance int 4 0 Y N Y Y N Distance from the 3 prime end of the biosequence BS_feature 6 sequence_length Sequence Length int 4 0 Y N Y Y N Length of oligonucleotide reporter BS_feature 7 feature_sequence Feature Sequence varchar 1024 0 Y N Y Y N Length of oligonucleotide reporter BS_feature 8 n_blast_matches Number of BLAST matches int 4 0 Y N Y Y N Number of BLAST matches for this reporter BS_feature_hit 1 feature_id Feature ID int 4 0 N Y N N Y pkDEFAULT BS_feature_hit 2 biosequence_id Biosequence ID int 4 0 N N N N N BS_feature_hit 3 expect_value Expect Value float 8 0 Y N Y Y N E value for BLAST BS_feature_hit 4 score Score real 4 0 Y N Y Y N BLAST score BS_feature_hit 5 number_of_identities Number of Identities int 4 0 Y N Y Y N Number of identities from BLAST BS_feature_hit 6 hit_sequence Hit Sequence varchar 1024 0 Y N Y Y N Sequence of BLAST hit BS_filterblast_statistic 1 biosap_search_id BIOSAP Search ID int 4 0 N Y N N Y pkDEFAULT BS_filterblast_statistic 2 filter_blast_version FilterBlast Version varchar 50 0 Y N N N N Version of FilterBlast BS_filterblast_statistic 3 n_unique_features Number of Unique Features int 4 0 Y N Y Y N Number of unique reporters found BS_filterblast_statistic 4 n_multiple_features Number of Multiple Features int 4 0 Y N Y Y N Number of multiple reporters found BS_query_option 1 query_option_id Query Option ID int 4 0 N Y N N Y BS_query_option 2 option_type Option Type varchar 255 0 Y N Y Y N BS_query_option 3 option_key Option Key varchar 255 0 Y N Y Y N BS_query_option 4 option_value Option Value varchar 255 0 Y N Y Y N BS_query_option 5 sort_order Sort Order int 10 0 Y N N N N BS_query_option 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N BS_query_option 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N N BS_query_option 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N BS_query_option 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N N BS_query_option 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N N BS_query_option 11 record_status Record Status char 1 0 N N N N N N BrowseBioSapFeature 1 biosap_search_id BioSap Run N optionlist 4 Y Y N Select BioSap to pull features from SELECT biosap_search_id, biosap_search_idcode FROM $TBBS_BIOSAP_SEARCH pkDEFAULT BrowseBioSapFeature 2 tm_constraint Tm Constraint N text 40 Y Y N Constraint for the Melting Temperature. Allowed syntax: "n.n", "> n.n", "< n.n", "between n.n and n.n", "n.n +- n.n" BrowseBioSapFeature 3 threeprime_distance_constraint 3' Distance Constraint N text 40 Y Y N Constraint for the 3' Distance. Allowed syntax: "n", "> n", "< n", "between n and n", "n +- n" BrowseBioSapFeature 4 mismatch_rejection_constraint Mismatch Rejection Constraint N text 40 Y Y N Constraint for the number of maximum number of mismatches to reject (e.g. if 2 is specified, then any feature that matches more than one gene with up to 2 mismatched base pairs will be rejected) BrowseBioSapFeature 5 biosequence_name_constraint BioSequence Names N textarea 5 Y Y N You may list a subset of genes to include in the output list instead of all found genes. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. BrowseBioSapFeature 6 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 $TBBS_QUERY_OPTION WHERE option_type = 'BBSF_sort_options' ORDER BY sort_order,option_value BrowseBioSapFeature 7 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options SELECT option_key,option_value FROM $TBBS_QUERY_OPTION WHERE option_type = 'BBSF_display_options' ORDER BY sort_order,option_value BrowseBioSapFeature 8 row_limit Maximum Rows N text 10 Y Y N Limit the numbers of rows displayed. If not provided, default is 5000 rows. BS_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 $TBBS_BIOSEQUENCE_SET ORDER BY sort_order,set_name pkDEFAULT BS_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. BS_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. BS_BrowseBioSequence 4 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. BS_BrowseBioSequence 5 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. BS_BrowseBioSequence 6 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 $TBBS_QUERY_OPTION WHERE option_type = 'BBS_sort_options' ORDER BY sort_order,option_value BS_BrowseBioSequence 7 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options SELECT option_key,option_value FROM $TBBS_QUERY_OPTION WHERE option_type = 'BBS_display_options' ORDER BY sort_order,option_value BS_BrowseBioSequence 8 row_limit Maximum Rows N text 10 Y Y N Limit the numbers of rows displayed. If not provided, default is 100 rows. BS_biosequence_set 1 biosequence_set_id BioSequence Set ID int 4 0 N Y N N pkDEFAULT BS_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 BS_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 BS_biosequence_set 4 set_name Set Name varchar 100 0 N N Y text 50 Y Y N Name of this BioSequence database BS_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 BS_biosequence_set 6 set_description Set Description varchar 255 0 N N Y text 50 Y Y N Longer description of this BioSequence database BS_biosequence_set 7 set_version Set Version varchar 50 0 N N Y text 40 Y Y N Version of this BioSequence database BS_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 BS_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 BS_biosequence_set 10 set_path Set Path varchar 255 0 N N Y text 50 Y Y N File path of this BioSequence database BS_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 BS_biosequence_set 12 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF BS_biosequence_set 13 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments BS_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. BS_biosequence_set 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N BS_biosequence_set 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N BS_biosequence_set 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N BS_biosequence_set 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N BS_biosequence_set 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N BS_biosequence_set 20 record_status Record Status char 1 0 N N N N N BS_dbxref 1 dbxref_id dbxref ID int 4 0 N Y N N N pkDEFAULT BS_dbxref 2 dbxref_name CrossRef Name varchar 50 0 N N Y text 40 Y Y N Name of this Database Cross Reference BS_dbxref 3 dbxref_tag CrossRef Tag varchar 20 0 N N Y text 20 Y Y Y Short tag (name) of this Database Cross Reference BS_dbxref 4 dbxref_description Description varchar 255 0 N N Y text 50 Y Y N Longer description of this Database Cross Reference BS_dbxref 5 accessor Accessor varchar 255 0 N N Y text 50 Y Y N Part of a URL or URI to which an accession number can be appended to get more information about the entity using this cross reference BS_dbxref 6 accessor_suffix Accessor Suffix varchar 255 0 Y N N text 50 Y Y N Part of a URL or URI which comes after the accession number to build the full URL to get more information about the entity using this cross reference BS_dbxref 7 uri URI varchar 255 0 N N Y text 50 Y Y N External web page or other URI of the database SELF BS_dbxref 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments BS_dbxref 9 sort_order Sort Order int 4 0 N 10 N N N N BS_dbxref 10 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N BS_dbxref 11 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N N BS_dbxref 12 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N BS_dbxref 13 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N N BS_dbxref 14 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N N BS_dbxref 15 record_status Record Status char 1 0 N N N N N N BS_biosequence 1 biosequence_id BioSequence ID int 4 0 N Y N N Y pkDEFAULT BS_biosequence 2 biosequence_set_id BioSequence Set int 4 0 N N PR_biosequence_set biosequence_set_id N N Y BioSequence Set to which this BioSequence belongs pkDEFAULT BS_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) BS_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 BS_biosequence 5 dbxref_id Database Cross Reference int 4 0 Y N PR_dbxref dbxref_id Y Y N Database cross reference for which the accession number applies pkDEFAULT BS_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 BS_biosequence 7 biosequence_desc Biosequence Description varchar 1024 0 N N Y textarea 5 Y Y N Description of this BioSequence (generally everything after the first space in a FASTA file header line) BS_biosequence 8 biosequence_seq Sequence text 16 0 Y N N file 40 Y Y N Actual sequence of the BioSequence if known BS_biosequence_property_set 1 biosequence_property_set_id BioSequence Property Set ID int 4 0 N Y N N N pkDEFAULT BS_biosequence_property_set 2 biosequence_id BioSequence ID int 4 0 N N PR_biosequence biosequence_id N N Y Biosequence to which this Biosequence property set belongs pkDEFAULT BS_biosequence_property_set 3 n_transmembrane_regions Number of Transmembrane Regions int 4 0 Y N Y Y N Number of transmembrane regions pkDEFAULT BS_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 BS_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 BS_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) BS_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 BS_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 BS_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? BS_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 BS_biosequence_property_set 11 chromosome Chromosome varchar 50 0 Y N N text 50 Y Y N Chromosome in which this mapping occurs BS_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 BS_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 BS_biosequence_property_set 14 strand Strand char 1 0 Y N N text 10 Y Y N Strand (+,-) of the biosequence in the chromosome