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 SN_biosequence_set 1 biosequence_set_id BioSequence Set ID int 4 0 N Y N N pkDEFAULT SN_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 SN_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 SN_biosequence_set 4 set_name Set Name varchar 100 0 N N Y text 50 Y Y N Name of this BioSequence database SN_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 SN_biosequence_set 6 set_description Set Description varchar 255 0 N N Y text 50 Y Y N Longer description of this BioSequence database SN_biosequence_set 7 set_version Set Version varchar 50 0 N N Y text 40 Y Y N Version of this BioSequence database SN_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 SN_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 SN_biosequence_set 10 set_path Set Path varchar 255 0 N N Y text 50 Y Y N File path of this BioSequence database SN_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 SN_biosequence_set 12 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF SN_biosequence_set 13 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_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. SN_biosequence_set 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_biosequence_set 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N SN_biosequence_set 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_biosequence_set 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N SN_biosequence_set 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_biosequence_set 20 record_status Record Status char 1 0 N N N N N SN_biosequence 1 biosequence_id BioSequence ID int 4 0 N Y N N N pkDEFAULT SN_biosequence 2 biosequence_set_id BioSequence Set ID int 4 0 N N SN_biosequence_set biosequence_set_id Y optionlist 20 Y Y Y The BioSequence Set from which this BioSequnce come from "SELECT biosequence_set_id, organism_id FROM $TB_BIOSEQUENCE_SET WHERE record_status != 'D' ORDER BY sort_order, organism_id" SN_biosequence 3 biosequence_name BIoSequence Name varchar 50 0 N N Y text 20 Y Y Y Name for the BioSequence (i.e. Gene/Cassette Name) SN_biosequence 4 biosequence_gene_name BioSequence Gene Name varchar 50 0 Y N N text 20 Y Y N The Common Name for the BioSequence SN_biosequence 5 biosequence_acession BioSequence Accession varchar 8 0 Y N N text 20 Y Y N The Accession Number for this BioSequnce (if available) SN_biosequence 6 biosequence_desc BioSequence Description varchar 255 0 Y N N text 20 Y Y N A description SN_biosequence 7 biosequence_start BioSequence Start int 4 0 N N Y text 20 Y Y N The start coor SN_biosequence 8 biosequence_length BioSequence Length int 4 0 N N Y text 20 Y Y N The length in bp SN_biosequence 9 biosequence_seq BioSequence Sequence text 16 0 Y N N textarea 4 Y Y N "The sequence, if present" SN_biosequence 10 biosequence_build_info BioSequence Build/Vesion Info varchar 255 0 Y N N text 20 Y Y N "Information about the assembly build, if needed" SN_biosequence 11 inherit_from_biosequence_id Inherited BioSequence int 4 0 Y N biosequence_id N optionlist Y Y N "The Inherited BioSequence (if this has a ""parent"" sequence)" "SELECT biosequnce_id, biosequence_name FROM $TB_BIOSEQUENCE WHERE record_status != 'D' ORDER BY biosequence_name" SN_biosequence 12 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_biosequence 13 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_biosequence 14 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_biosequence 15 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_biosequence 16 record_status Record Status char 1 0 N N N N N SN_biosequence_property_set 1 biosequence_property_set_id BioSequence Property Set ID int 4 0 N Y N N pkDEFAULT SN_biosequence_property_set 2 biosequence_id BioSequence ID int 4 0 N N SN_biosequence biosequence_id N N Y Biosequence to which this Biosequence property set belongs SN_biosequence_property_set 3 n_transmembrane_regions Number of Transmembrane Regions int 4 0 Y N Y Y N Number of transmembrane regions SN_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" SN_biosequence_property_set 5 transmembrane_topology Transmembrane Region Topology text 16 0 Y N Y text 20 Y Y N Coding of which residues belong in the transmembrane regions SN_biosequence_property_set 6 starting_offset Starting Offset int 4 0 Y N Y text 20 Y Y N "Absolute offset of the start of this sequence within some reference, usually the chromosome" SN_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 $TBSN_BIOSEQUENCE_SET ORDER BY sort_order,set_name" SN_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. SN_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. SN_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. SN_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. SN_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 $TBSN_QUERY_OPTION WHERE option_type = 'BBS_sort_options' ORDER BY sort_order,option_value" SN_BrowseBioSequence 7 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'BBS_display_options' ORDER BY sort_order,option_value" SN_BrowseBioSequence 8 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." SN_snp_source 1 snp_source_id SNP Source ID int 4 0 N Y N N pkDEFAULT SN_snp_source 2 source_name Source Name varchar 25 0 N N Y text 25 Y Y Y Name of the direct source of this SNP SN_snp_source 3 orig_source_name Original Source Name varchar 25 0 N N N text 25 Y Y Y Name of the original origin of this SNP (perhaps via someone else's curation as listed above) SN_snp_source 4 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF SN_snp_source 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_snp_source 6 sort_order Sort Order int 4 0 N 10 N N N N SN_snp_source 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_snp_source 8 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_snp_source 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_snp_source 10 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_snp_source 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_snp_source 12 record_status Record Status char 1 0 N N N N N SN_BrowseSNPHit 1 snp_accession_constraint SNP Accession N text 20 Y Y N Constraint for the main SNP accession. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_BrowseSNPHit 2 snp_source_accession_constraint SNP Source Accession N text 20 Y Y N Constraint for the SNP accession from the original source. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_BrowseSNPHit 3 snp_source_id SNP Source N multioptionlist 4 Y Y N "Select desired SNP sources to include in query. Multiple items may be selected. If no items are selected, ALL sets are searched." "SELECT snp_source_id,source_name+' - '+orig_source_name FROM $TBSN_SNP_SOURCE ORDER BY sort_order,source_name" SN_BrowseSNPHit 4 biosequence_set_id BioSequence Set 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 $TBSN_BIOSEQUENCE_SET WHERE record_status != 'D' ORDER BY sort_order,set_name" SN_BrowseSNPHit 5 identified_percent_constraint Identified Percent N text 20 Y Y N "Constraint for the percentage (00 to 100) of identified base pairs. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"" or ""n.n +- n.n""" SN_BrowseSNPHit 6 match_to_query_ratio_constraint Match to Query Ratio N text 20 Y Y N "Constraint for how much of the query was matched as a percentage (00 to 100) of the total query length. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"" or ""n.n +- n.n""" SN_BrowseSNPHit 7 validation_status_constraint Validation Status N multioptionlist 4 Y Y N "Constraint for the validation status of the snp_instance. If no items are selected, ALL validation statuses are searched." "SELECT distinct(validation_status) INTO #tmpval FROM $TBSN_SNP_INSTANCE ORDER BY validation_status SELECT validation_status,validation_status FROM #tmpval" SN_BrowseSNPHit 8 threeprime_flanking_length_constraint 3' Flanking Length N text 20 Y Y N "Constraint for the length of the 3' flanking length. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"" or ""n.n +- n.n""" SN_BrowseSNPHit 9 fiveprime_flanking_length_constraint 5' Flanking Length N text 20 Y Y N "Constraint for the length of the 5' flanking length. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"" or ""n.n +- n.n""" SN_BrowseSNPHit 10 snp_location_constraint SNP Location N text 20 Y Y N "Absolute location on the chromosome of the SNPs. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"" or ""n.n +- n.n""" SN_BrowseSNPHit 11 snp_selection_options Special Selection Options N multioptionlist 4 Y Y N Special SNP selection options. Multiple options or none may be selected. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'BSH_selection_options' ORDER BY sort_order,option_value" SN_BrowseSNPHit 12 biosequence_rank_list_id BioSequence Rank List N multioptionlist 4 Y Y N "Select a BioSequence Rank List to prioritize result listing. If no item is selected, no ranking is done." "SELECT biosequence_rank_list_id,username+' - '+rank_list_name FROM $TBSN_BIOSEQUENCE_RANK_LIST BRL LEFT JOIN $TB_USER_LOGIN UL ON (BRL.created_by_id = UL.contact_id) WHERE BRL.record_status != 'D' ORDER BY username,rank_list_name" SN_BrowseSNPHit 13 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'BSH_display_options' ORDER BY sort_order,option_value" SN_BrowseSNPHit 14 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." SN_source_version 1 source_version_id Source Version ID int 4 0 N Y N N pkDEFAULT SN_source_version 2 source_version_name Source Version Name varchar 255 0 N N Y text 50 Y Y Y Name of the version of the source dataset (e.g. Celera MHC 2002-04-01) SN_source_version 3 uri URI varchar 255 0 Y N N text 50 Y Y N "External web page, file, or other URI" SELF SN_source_version 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_source_version 5 sort_order Sort Order int 4 0 N 10 N N N N SN_source_version 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_source_version 7 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_source_version 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_source_version 9 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_source_version 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_source_version 11 record_status Record Status char 1 0 N N N N N SN_biosequence_rank_list 1 biosequence_rank_list_id BioSequence Rank List int 4 0 N Y N N pkDEFAULT SN_biosequence_rank_list 2 rank_list_name Rank List Name varchar 255 0 N N Y text 50 Y Y Y Name of the list of ranked biosequences (as it will appear in a drop-down list) SN_biosequence_rank_list 3 rank_list_file Rank List File varchar 255 0 N N N file 30 Y Y N Hit [Browse] and specify the tab-delimited text file which contains the ranking information. This must be in the correct format. SN_biosequence_rank_list 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments about this rank list SN_biosequence_rank_list 5 sort_order Sort Order int 4 0 N 10 N N N N SN_biosequence_rank_list 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_biosequence_rank_list 7 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_biosequence_rank_list 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_biosequence_rank_list 9 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_biosequence_rank_list 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_biosequence_rank_list 11 record_status Record Status char 1 0 N N N N N SN_snp_plate 1 plate_id Plate ID int 4 0 N Y N N pkDEFAULT SN_snp_plate 2 contact_id Contact int 4 0 N N contact contact_id Y current_contact_id Y Y N PI for this plate SN_snp_plate 3 project_id Project int 4 0 N N project project_id Y optionlist Y Y N Project to which the plate belongs "SELECT project_id, name + ' ['+budget+']' FROM $TB_PROJECT WHERE PI_contact_id='$contact_id' ORDER BY name" SN_snp_plate 4 plate_name Plate Title varchar 100 0 N N Y text 50 Y Y N Title of this plate SN_snp_plate 5 plate_tag Plate Tag varchar 20 0 N N Y text 20 Y Y Y Short tag (name) of this plate. Treat this like a directory/folder name. Do not use spaces or non-standard characters. SN_snp_plate 6 plate_description Plate Description text 16 0 N N Y textarea 6 Y Y N "Description of this experiment, the sample or samples used, and any other relevant information not contained in the project description or in list-box elements in this form" SN_snp_plate 7 plate_path Plate Path varchar 255 0 N N Y text 50 Y Y N Data path for this plate (e.g. /data/search/edeutsch/TCells/T_000/human_nci) SN_snp_plate 8 organism_id Organism int 4 0 N N Y optionlist Y Y N Organism from which the sample used for this plate was derived "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" SN_snp_plate 9 plate_type_id Plate Type int 4 0 N N Y optionlist Y Y N Type of plate "SELECT plate_type_id, plate_type_name FROM $TBSN_PLATE_TYPE ORDER BY sort_order,plate_type_name" SN_snp_plate 10 instrument_id Instrument int 4 0 N N Y optionlist Y Y N Instrument on which this plate was run "SELECT instrument_id, instrument_name FROM $TBSN_INSTRUMENT ORDER BY sort_order,instrument_name" SN_snp_plate 11 go_public_date Go Public Date datetime 8 0 Y CURRENT_TIMESTAMP N N text 20 Y Y N Date that this plate data will go public. Please use the form 2002-12-31. Do not enter a date higher than 2030-01-01. SN_snp_plate 12 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF SN_snp_plate 13 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_snp_plate 14 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_snp_plate 15 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N SN_snp_plate 16 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_snp_plate 17 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N SN_snp_plate 18 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_snp_plate 19 record_status Record Status char 1 0 N N N N N SN_plate_type 1 plate_type_id Plate Type ID int 4 0 N Y N N pkDEFAULT SN_plate_type 2 plate_type_name Plate Type Name varchar 100 0 N N Y text 20 Y Y Y Short name of this plate type as it will appear in list boxes SN_plate_type 3 plate_type_description Plate Type Description varchar 255 0 N N Y text 50 Y Y N More complete description of this plate type SN_plate_type 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_plate_type 5 sort_order Sort Order int 2 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box SN_plate_type 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_plate_type 7 created_by_id Record Created By int 2 0 N 1 N contact contact_id N N SN_plate_type 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_plate_type 9 modified_by_id Record Modified By int 2 0 N 1 N contact contact_id N N SN_plate_type 10 owner_group_id Owner Group ID int 2 0 N 1 N work_group work_group_id N N SN_plate_type 11 record_status Record Status char 1 0 N N N N N SN_instrument_type 1 instrument_type_id Instrument Type ID int 4 0 N Y N N pkDEFAULT SN_instrument_type 2 instrument_type_name Instrument Type Name varchar 100 0 N N Y text 20 Y Y Y Short name of this instrument type as it will appear in list boxes SN_instrument_type 3 instrument_type_description Instrument Type Description varchar 255 0 N N Y text 50 Y Y N More complete description of this instrument type SN_instrument_type 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_instrument_type 5 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box SN_instrument_type 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_instrument_type 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N SN_instrument_type 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_instrument_type 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N SN_instrument_type 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_instrument_type 11 record_status Record Status char 1 0 N N N N N SN_instrument 1 instrument_id Instrument ID int 4 0 N Y N N pkDEFAULT SN_instrument 2 instrument_type_id Instrument Type int 4 0 N N SN_instrument_type instrument_type_id Y optionlist Y Y N Type of Instrument "SELECT instrument_type_id,instrument_type_name FROM $TBSN_INSTRUMENT_TYPE ORDER BY sort_order,instrument_type_name" SN_instrument 3 instrument_name Instrument Name varchar 100 0 N N Y text 30 Y Y Y Short name of this instrument as it will appear in list boxes SN_instrument 4 instrument_description Instrument Description varchar 255 0 N N Y text 60 Y Y N More complete description of this instrument SN_instrument 5 comment Comment text 16 0 Y N N textarea 10 Y Y N Additional comments SN_instrument 6 sort_order Sort Order int 4 0 N 10 N Y text 10 Y Y N Numbers which override alphabetical sorting in a list box SN_instrument 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_instrument 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N SN_instrument 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_instrument 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N SN_instrument 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_instrument 12 record_status Record Status char 1 0 N N N N N SN_GetGenotypes 1 project_id Project N multioptionlist 4 refreshDocument() Y Y N Select desired projects to query. Multiple items may be selected. "SELECT distinct project_id,project_id FROM SNP.dbo.export_results_view ORDER BY project_id" SN_GetGenotypes 2 plate_id_constraint Plate ID N multioptionlist 4 Y Y N Select desired plates to query. Multiple items may be selected. "SELECT distinct plate_pk,plate_id FROM SNP.dbo.export_results_view WHERE project_id IN ( $parameters{project_id} ) ORDER BY plate_id" SN_GetGenotypes 3 assay_id_constraint Assay ID N text 40 Y Y N Constraint for assay name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes 4 sample_id_constraint Sample ID N text 40 Y Y N Constraint for sample name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes 5 minor_allele_limit Minor Allele Limit 0.1 N text 40 Y Y N "Set cutoff value for flagging low minor allele frequencies. Acceptable range is [0,1]." SN_GetGenotypes 6 description Call Quality N multioptionlist 4 Y Y N Select desired genotype quality level. Multiple items may be selected. "SELECT distinct description,description FROM SNP.dbo.export_results_view ORDER BY description" SN_GetGenotypes 7 assay_order_list_id Assay Order List N multioptionlist 4 Y Y N "Select an Assay Order List to sort result listing (useful in Sample vs. Assay). If no item is selected, no ranking is done." "SELECT assay_order_list_id,username+' - '+assay_order_list_name FROM $TBSN_ASSAY_ORDER_LIST AOL LEFT JOIN $TB_USER_LOGIN UL ON (AOL.created_by_id = UL.contact_id) WHERE AOL.record_status != 'D' ORDER BY username,assay_order_list_name" SN_GetGenotypes 8 view_style View Style N optionlist Y Y N Select desired data view. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_view_style' ORDER BY sort_order,option_value" SN_GetGenotypes 9 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options. Multiple items may be selected. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_display_options' ORDER BY sort_order,option_value" SN_GetGenotypes_Vietnam 1 project_id Project N multioptionlist 4 refreshDocument() Y Y N Select desired projects to query. Multiple items may be selected. "SELECT distinct project_id,project_id FROM SNP.dbo.export_results_view ORDER BY project_id" SN_GetGenotypes_Vietnam 2 plate_id_constraint Plate ID N multioptionlist 4 Y Y N Select desired plates to query. Multiple items may be selected. "SELECT distinct plate_pk,plate_id FROM SNP.dbo.export_results_view WHERE project_id IN ( $parameters{project_id} ) ORDER BY plate_id" SN_GetGenotypes_Vietnam 3 assay_id_constraint Assay ID N text 40 Y Y N Constraint for assay name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes_Vietnam 4 sample_id_constraint Sample ID N text 40 Y Y N Constraint for sample name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes_Vietnam 5 minor_allele_limit Minor Allele Limit 0.1 N text 40 Y Y N "Set cutoff value for flagging low minor allele frequencies. Acceptable range is [0,1]." SN_GetGenotypes_Vietnam 6 description Call Quality N multioptionlist 4 Y Y N Select desired genotype quality level. Multiple items may be selected. "SELECT distinct description,description FROM SNP.dbo.export_results_view ORDER BY description" SN_GetGenotypes_Vietnam 7 assay_order_list_id Assay Order List N multioptionlist 4 Y Y N "Select an Assay Order List to sort result listing (useful in Sample vs. Assay). If no item is selected, no ranking is done." "SELECT assay_order_list_id,username+' - '+assay_order_list_name FROM $TBSN_ASSAY_ORDER_LIST AOL LEFT JOIN $TB_USER_LOGIN UL ON (AOL.created_by_id = UL.contact_id) WHERE AOL.record_status != 'D' ORDER BY username,assay_order_list_name" SN_GetGenotypes_Vietnam 8 view_style View Style N optionlist Y Y N Select desired data view. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_view_style' ORDER BY sort_order,option_value" SN_GetGenotypes_Vietnam 9 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options. Multiple items may be selected. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_display_options' ORDER BY sort_order,option_value" SN_GetGenotypes_Ian5 1 project_id Project N multioptionlist 4 refreshDocument() Y Y N Select desired projects to query. Multiple items may be selected. "SELECT distinct project_id,project_id FROM SNP.dbo.export_results_view ORDER BY project_id" SN_GetGenotypes_Ian5 2 plate_id_constraint Plate ID N multioptionlist 4 Y Y N Select desired plates to query. Multiple items may be selected. "SELECT distinct plate_pk,plate_id FROM SNP.dbo.export_results_view WHERE project_id IN ( $parameters{project_id} ) ORDER BY plate_id" SN_GetGenotypes_Ian5 3 assay_id_constraint Assay ID N text 40 Y Y N Constraint for assay name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes_Ian5 4 sample_id_constraint Sample ID N text 40 Y Y N Constraint for sample name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes_Ian5 5 minor_allele_limit Minor Allele Limit 0.1 N text 40 Y Y N "Set cutoff value for flagging low minor allele frequencies. Acceptable range is [0,1]." SN_GetGenotypes_Ian5 6 description Call Quality N multioptionlist 4 Y Y N Select desired genotype quality level. Multiple items may be selected. "SELECT distinct description,description FROM SNP.dbo.export_results_view ORDER BY description" SN_GetGenotypes_Ian5 7 assay_order_list_id Assay Order List N multioptionlist 4 Y Y N "Select an Assay Order List to sort result listing (useful in Sample vs. Assay). If no item is selected, no ranking is done." "SELECT assay_order_list_id,username+' - '+assay_order_list_name FROM $TBSN_ASSAY_ORDER_LIST AOL LEFT JOIN $TB_USER_LOGIN UL ON (AOL.created_by_id = UL.contact_id) WHERE AOL.record_status != 'D' ORDER BY username,assay_order_list_name" SN_GetGenotypes_Ian5 8 view_style View Style N optionlist Y Y N Select desired data view. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_view_style' ORDER BY sort_order,option_value" SN_GetGenotypes_Ian5 9 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options. Multiple items may be selected. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_display_options' ORDER BY sort_order,option_value" SN_GetGenotypes_Ian5-Extended 1 project_id Project N multioptionlist 4 refreshDocument() Y Y N Select desired projects to query. Multiple items may be selected. "SELECT distinct project_id,project_id FROM SNP.dbo.export_results_view ORDER BY project_id" SN_GetGenotypes_Ian5-Extended 2 plate_id_constraint Plate ID N multioptionlist 4 Y Y N Select desired plates to query. Multiple items may be selected. "SELECT distinct plate_pk,plate_id FROM SNP.dbo.export_results_view WHERE project_id IN ( $parameters{project_id} ) ORDER BY plate_id" SN_GetGenotypes_Ian5-Extended 3 assay_id_constraint Assay ID N text 40 Y Y N Constraint for assay name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes_Ian5-Extended 4 sample_id_constraint Sample ID N text 40 Y Y N Constraint for sample name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. SN_GetGenotypes_Ian5-Extended 5 minor_allele_limit Minor Allele Limit 0.1 N text 40 Y Y N "Set cutoff value for flagging low minor allele frequencies. Acceptable range is [0,1]." SN_GetGenotypes_Ian5-Extended 6 description Call Quality N multioptionlist 4 Y Y N Select desired genotype quality level. Multiple items may be selected. "SELECT distinct description,description FROM SNP.dbo.export_results_view ORDER BY description" SN_GetGenotypes_Ian5-Extended 7 assay_order_list_id Assay Order List N multioptionlist 4 Y Y N "Select an Assay Order List to sort result listing (useful in Sample vs. Assay). If no item is selected, no ranking is done." "SELECT assay_order_list_id,username+' - '+assay_order_list_name FROM $TBSN_ASSAY_ORDER_LIST AOL LEFT JOIN $TB_USER_LOGIN UL ON (AOL.created_by_id = UL.contact_id) WHERE AOL.record_status != 'D' ORDER BY username,assay_order_list_name" SN_GetGenotypes_Ian5-Extended 8 view_style View Style N optionlist Y Y N Select desired data view. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_view_style' ORDER BY sort_order,option_value" SN_GetGenotypes_Ian5-Extended 9 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options. Multiple items may be selected. "SELECT option_key,option_value FROM $TBSN_QUERY_OPTION WHERE option_type = 'GG_display_options' ORDER BY sort_order,option_value" SN_snp_selection_run 1 snp_selection_run_id SNP Selection Run ID int 4 0 N Y Y SN_snp_selection_run 2 snp_selection_run_name SNP Selection Run Name varchar 255 0 N N Y text 50 Y Y Y Name of this SNP selection run SN_snp_selection_run 3 snp_selection_run_description SNP Selection Run Description text 16 0 N N Y textarea 4 Y Y N "Description of this SNP selection run (e.g., 'Primary Selection for JDRF Chr. 10', 'Extra SNPs for JDRF Chr. 10')" SN_snp_selection_run 4 run_date SNP Selection Run Date datetime 8 0 N CURRENT_TIMESTAMP N Y textdate 20 Y Y N Date of this SNP selection run SN_snp_selection_run 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_snp_selection_run 6 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_snp_selection_run 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_snp_selection_run 8 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_snp_selection_run 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_snp_selection_run 10 record_status Record Status char 1 0 N N N N N N SN_status 1 status_id Status ID int 4 0 N Y N N pkDEFAULT SN_status 2 status_name Status Name text 4 0 N N Y text 50 Y Y Y "SNP status name: Library, Picked, Failed Design, Failed Constant" SN_status 3 status_description Status Description text 16 0 N N Y textarea 4 Y Y N Longer description of the SNP status SN_status 3 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_status 4 sort_order Sort Order int 4 0 N 10 N N N N SN_status 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_status 6 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_status 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_status 8 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_status 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_status 10 record_status Record Status char 1 0 N N N N N SN_selected_snp 1 selected_snp_id Selected SNP ID varchar 255 0 N Y SN_snp snp_id Y text 40 Y SN_selected_snp 2 snp_selection_run_id SNP Selection Run ID int 4 0 N N SN_snp_selection_run snp_selection_run_id Y Y Y N SN_selected_snp 3 jared_id Jared Roach ID varchar 255 0 N N N text 40 Y Y N ID for this SNP from Jared's merging SN_selected_snp 4 snp_id SNP ID int 4 0 N N Y Y Y N SN_selected_snp 5 position SNP Position int 4 0 N N Y Y Y N "Position of this SNP, relative to the biosquence" SN_selected_snp 6 quality_score Quality Score int 4 0 N N Y text 40 Y Y N SN_selected_snp 7 sequence SNP Sequence text 16 0 N N Y Y Y N SN_selected_snp 8 sequence_is_modified Original Sequence Modified? varchar 1 0 N N Y Y Y N Has the original sequence been mofidied? Usually from merged nearby SNPs. SN_selected_snp 9 status Status text 4 0 N N SN_status description Y text 40 Y Y N "Current status of this SNP. Valid codes are 'Library', 'Picked', 'Failed design', 'Failed constant'" SN_selected_snp 10 parent_gene_biosequence_id Parent Gene Biosequence ID int 4 0 N N Y Y Y N SN_selected_snp 11 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_selected_snp 12 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_selected_snp 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_selected_snp 14 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_selected_snp 15 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_selected_snp 16 record_status Record Status char 1 0 N N N N N SN_replaced_snp 1 snp_id SNP ID int 4 0 N N SN_snp snp_id Y Y Y Y SNP ID of the chosed replacement SNP SN_replaced_snp 2 snp_selection_run_id SNP Selection Run ID int 4 0 N N SN_snp_selection_run snp_selection_run_id Y Y Y Y SNP Selection Run of the replacement SN_replaced_snp 3 replaced_snp_id Replaced SNP ID int 4 0 N N Y Y Y Y SNP ID of the SNP that has been replaced SN_manual_genotype_call 1 manual_genotype_call_id Manual Genotype Call ID int 4 0 N Y N N SN_manual_genotype_call 2 project_label Project varchar 255 0 N N Y fixed Y Y Y Project to which the genotype call belongs SN_manual_genotype_call 3 assay_id Assay ID varchar 255 0 N N Y fixed Y Y Y Assay of the genotype call SN_manual_genotype_call 4 sample_id Sample ID varchar 255 0 N N Y fixed Y Y Y Sample ID SN_manual_genotype_call 5 genotype_call Genotype Call varchar 20 0 N N Y text 10 Y Y N "Genotype call in a form like T/T or T/C, etc." SN_manual_genotype_call 6 call_quality Call Quality varchar 255 0 N N Y optionlist Y Y N Genotype call quality "SELECT distinct description,description FROM SNP.dbo.export_results_view ORDER BY description" SN_manual_genotype_call 7 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments SN_manual_genotype_call 8 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_manual_genotype_call 9 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_manual_genotype_call 10 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_manual_genotype_call 11 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_manual_genotype_call 12 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_manual_genotype_call 13 record_status Record Status char 1 0 N N N N N N SN_assay_order_list 1 assay_order_list_id Assay Order List int 4 0 N Y N N pkDEFAULT SN_assay_order_list 2 assay_order_list_name Assay Order List Name varchar 255 0 N N Y text 50 Y Y Y Name of the list of ordered assays (as it will appear in a drop-down list) SN_assay_order_list 3 assay_order_list_file Assay Order List File varchar 255 0 N N N file 30 Y Y N Hit [Browse] and specify the tab-delimited text file which contains the assay position information. This must be in the correct format. SN_assay_order_list 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments about this assay order list SN_assay_order_list 5 sort_order Sort Order int 4 0 N 10 N N N N SN_assay_order_list 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N SN_assay_order_list 7 created_by_id Record Created By int 4 0 N N contact contact_id N N SN_assay_order_list 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N SN_assay_order_list 9 modified_by_id Record Modified By int 4 0 N N contact contact_id N N SN_assay_order_list 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N SN_assay_order_list 11 record_status Record Status char 1 0 N N N N N