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 IS_abundance_level 1 abundance_level_id AbundanceLevel ID int 4 0 N Y N N pkDEFAULT IS_abundance_level 2 abundance_level_name Abundance Level Name varchar 50 0 N N Y text 20 Y Y Y Name of level of abundance of cell type IS_abundance_level 3 abundance_level_description Abundance Level Description varchar 256 0 N N Y text 50 Y Y N Longer description of this level IS_abundance_level 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_abundance_level 5 sort_order Sort Order int 4 0 N 10 N N text 1 Y Y N Integer designed to assist in sort records of this type IS_abundance_level 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_abundance_level 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_abundance_level 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_abundance_level 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_abundance_level 10 owner_group_id Owner Group ID datetime 8 0 N 1 N work_group work_group_id N N IS_abundance_level 11 record_status Record Status char 1 0 N N N N N IS_biosequence_set 1 biosequence_set_id BioSequence Set ID int 4 0 N Y N N pkDEFAULT IS_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" IS_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" IS_biosequence_set 4 set_name Set Name varchar 100 0 N N Y text 50 Y Y N Name of this BioSequence database IS_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 IS_biosequence_set 6 set_description Set Description varchar 255 0 N N Y text 50 Y Y N Longer description of this BioSequence database IS_biosequence_set 7 set_version Set Version varchar 50 0 N N Y text 40 Y Y N Version of this BioSequence database IS_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" IS_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 IS_biosequence_set 10 set_path Set Path varchar 255 0 N N Y text 50 Y Y N File path of this BioSequence database IS_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 IS_biosequence_set 12 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF IS_biosequence_set 13 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_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. IS_biosequence_set 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_biosequence_set 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_biosequence_set 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_biosequence_set 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_biosequence_set 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_biosequence_set 20 record_status Record Status char 1 0 N N N N N IS_dbxref 1 dbxref_id dbxref ID int 4 0 N Y N N pkDEFAULT IS_dbxref 2 dbxref_name CrossRef Name varchar 50 0 N N Y text 40 Y Y N Name of this Database Cross Reference IS_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 IS_dbxref 4 dbxref_description Description varchar 255 0 N N Y text 50 Y Y N Longer description of this Database Cross Reference IS_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 IS_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 IS_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 IS_dbxref 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_dbxref 9 sort_order Sort Order int 4 0 N 10 N N N N IS_dbxref 10 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_dbxref 11 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_dbxref 12 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_dbxref 13 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_dbxref 14 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_dbxref 15 record_status Record Status char 1 0 N N N N N IS_biosequence 1 biosequence_id BioSequence ID int 4 0 N Y N N pkDEFAULT IS_biosequence 2 biosequence_set_id BioSequence Set int 4 0 N N IS_biosequence_set biosequence_set_id N N Y BioSequence Set to which this BioSequence belongs pkDEFAULT IS_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) IS_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 IS_biosequence 5 dbxref_id Database Cross Reference int 4 0 Y N IS_dbxref dbxref_id Y Y N Database cross reference for which the accession number applies pkDEFAULT IS_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 IS_biosequence 7 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) IS_biosequence 8 biosequence_seq Sequence text 16 0 Y N N file 40 Y Y N Actual sequence of the BioSequence if known IS_query_option 1 query_option_id Query Option ID int 4 0 N Y N N pkDEFAULT IS_query_option 2 option_type Option Type varchar 255 0 N N Y text 50 Y Y Y Type or category of this option IS_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 IS_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 IS_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 IS_query_option 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_query_option 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_query_option 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_query_option 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_query_option 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_query_option 11 record_status Record Status char 1 0 N N N N N IS_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 $TBIS_BIOSEQUENCE_SET ORDER BY sort_order,set_name" IS_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. IS_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. IS_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. IS_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. IS_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. IS_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. IS_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""" IS_BrowseBioSequence 9 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y Y N "Constraint for the number of transmembrane regions (based on a 19-residue wide sliding window of hydropathy indexes above 1.58). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" IS_BrowseBioSequence 10 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. IS_BrowseBioSequence 11 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. IS_BrowseBioSequence 12 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 $TBIS_QUERY_OPTION WHERE option_type = 'BBS_sort_options' ORDER BY sort_order,option_value" IS_BrowseBioSequence 13 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBIS_QUERY_OPTION WHERE option_type = 'BBS_display_options' ORDER BY sort_order,option_value" IS_BrowseBioSequence 14 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 100 rows." IS_antibody 1 antibody_id Antibody ID int 4 0 N Y N N pkDEFAULT IS_antibody 2 antibody_name Antibody Name varchar 50 0 N N Y text 40 Y Y Y Name of this Antibody IS_antibody 3 antibody_description Antibody Description varchar 255 0 Y N N text 50 Y Y N Longer description of this Antibody IS_antibody 4 antigen_id Antigen int 4 0 N N IS_antigen antigen_id Y optionlist Y Y N Antigen that this antibody is recognized by "SELECT antigen_id, antigen_name FROM $TBIS_ANTIGEN ORDER BY sort_order,antigen_name" IS_antibody 5 protocol_id Preparation Protocol int 4 0 N N protocol protocol_id Y optionlist Y Y Y Protocol used to create this antibody "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE PT.name='Immunostain Slide Preparation' AND P.record_status != 'D' ORDER BY P.name" IS_antibody 6 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 6 Y Y N Describe any deviations from the intented above protocol to the way this preparation was actually executed IS_antibody 7 provider_contact_id Provider Contact int 4 0 Y N contact contact_id N optionlist Y Y Y Provider or vendor contact for obtaining this antibody "SELECT contact_id, first_name+' '+last_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY organization,last_name,first_name" IS_antibody 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_antibody 9 sort_order Sort Order int 4 0 N 1000 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_antibody 10 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_antibody 11 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_antibody 12 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_antibody 13 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_antibody 14 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_antibody 15 record_status Record Status char 1 0 N N N N N IS_antigen 1 antigen_id Antigen ID int 4 0 N Y N N pkDEFAULT IS_antigen 2 antigen_name Antigen Name varchar 50 0 N N Y text 40 Y Y Y Short name of this Antigen IS_antigen 3 alternate_names Alternate Names varchar 255 0 Y N N text 50 Y Y N Alternate names of this antigen IS_antigen 4 antigen_description Antigen Description varchar 255 0 Y N N text 50 Y Y N Longer description of this Antigen IS_antigen 5 biosequence_id Biosequence int 4 0 Y N IS_biosequence biosequence_id N optionlist Y Y N Biosequence entry (gene) that encodes for this antigen "SELECT biosequence_id, biosequence_name FROM $TBIS_BIOSEQUENCE ORDER BY biosequence_name" IS_antigen 6 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_antigen 7 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_antigen 8 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_antigen 9 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_antigen 10 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_antigen 11 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_antigen 12 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_antigen 13 record_status Record Status char 1 0 N N N N N IS_probe 1 probe_id Probe ID int 4 0 N Y N N pkDEFAULT IS_probe 2 probe_name Probe Name varchar 50 0 N N Y text 40 Y Y Y Name of this Probe IS_probe 3 probe_description Probe Description varchar 255 0 Y N N text 50 Y Y N Longer description of this Probe IS_probe 4 biosequence_id Biosequence int 4 0 Y N IS_biosequence biosequence_id N optionlist Y Y N Biosequence entry (gene) that encodes for this probe "SELECT biosequence_id, biosequence_name FROM $TBIS_BIOSEQUENCE ORDER BY biosequence_name" IS_probe 5 protocol_id Preparation Protocol int 4 0 N N protocol protocol_id Y optionlist Y Y Y Protocol used to create this probe "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE PT.name='Immunostain Slide Preparation' AND P.record_status != 'D' ORDER BY P.name" IS_probe 6 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 6 Y Y N Describe any deviations from the intented above protocol to the way this preparation was actually executed IS_probe 7 provider_contact_id Provider Contact int 4 0 Y N contact contact_id N optionlist Y Y Y Provider or vendor contact for obtaining this probe "SELECT contact_id, first_name+' '+last_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY organization,last_name,first_name" IS_probe 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_probe 9 sort_order Sort Order int 4 0 N 1000 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_probe 10 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_probe 11 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_probe 12 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_probe 13 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_probe 14 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_probe 15 record_status Record Status char 1 0 N N N N N IS_structural_unit 1 structural_unit_id Structural Unit ID int 4 0 N Y N N pkDEFAULT IS_structural_unit 2 structural_unit_name Structural Unit Name varchar 50 0 N N Y text 40 Y Y Y Name of this Cell Type IS_structural_unit 3 structural_unit_description Structural Unit Definition text 16 0 N N Y text 50 Y Y N Longer description of this Cell Type IS_structural_unit 4 ontology_term_id Ontology Term int 4 0 Y N ON_ontology_term ontology_term_id N optionlist Y Y N Ontology from which the term for this structural unit is selected IS_structural_unit 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_structural_unit 6 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_structural_unit 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_structural_unit 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_structural_unit 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_structural_unit 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_structural_unit 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_structural_unit 12 record_status Record Status char 1 0 N N N N N IS_expression_level 1 expression_level_id Expression Level ID int 4 0 N Y N N pkDEFAULT IS_expression_level 2 level_name Expression Level Name varchar 50 0 N N Y text 40 Y Y Y Name for the level of presence of a cell type IS_expression_level 3 level_definition Expression Level Definition varchar 255 0 N N Y textarea 3 Y Y N Definition of the expression_level IS_expression_level 4 weight weight real 4 0 N N Y text 20 Y Y N A value between 0 and 1 that dictates the weight that levels of this category get when combining data IS_expression_level 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_expression_level 6 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_expression_level 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_expression_level 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_expression_level 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_expression_level 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_expression_level 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_expression_level 12 record_status Record Status char 1 0 N N N N N IS_assay_unit_expression 1 assay_unit_expression_id Assay Unit Expression ID int 4 0 N Y N N pkDEFAULT IS_assay_unit_expression 2 assay_image_subfield_id Assay Image Subfield int 4 0 N N IS_assay_image_subfield assay_image_subfield_id N optionlist Y N Y Image subfield for this call is made "SELECT assay_image_subfield_id, subfield_name FROM $TBIS_ASSAY_IMAGE_SUBFIELD ORDER BY subfield_name" IS_assay_unit_expression 3 assay_image_id Assay Image int 4 0 N N IS_assay_image assay_image_id N optionlist Y N Y Image for this call is made "SELECT assay_image_id, image_name FROM $TBIS_ASSAY_IMAGE ORDER BY image_name" IS_assay_unit_expression 4 assay_channel_id Assay Channel int 4 0 N N IS_assay_channel assay_channel_id N optionlist Y N Y Assay channel (stain) for this call is made "SELECT assay_channel_id, ISNULL(ac.assay_channel_name,a.assay_name) + ' -chan ' + cast(ac.channel_index as varchar(1)) from $TBIS_ASSAY_CHANNEL ac join $TBIS_ASSAY a on ac.assay_id = a.assay_id" IS_assay_unit_expression 5 structural_unit_id Structural Unit int 4 0 N N IS_structural_unit structural_unit_id Y optionlist Y Y Y Cell type for this which this call is made "SELECT structural_unit_id, structural_unit_name FROM $TBIS_STRUCTURAL_UNIT ORDER BY sort_order,structural_unit_name" IS_assay_unit_expression 6 expression_level_id Expression Level int 4 0 Y N IS_expression_level expression_level_id Y optionlist Y Y N Level of expression for this cell type "SELECT expression_level_id, level_name FROM $TBIS_EXPRESSION_LEVEL ORDER BY sort_order,level_name" IS_assay_unit_expression 7 at_level_percent Percent Expressing at this Level real 4 0 Y N Y text 40 Y Y N A value between 0 and 100 that approximates the percentage of cells of of this type that are stained by the antibody/probe at the selected cell staining level IS_assay_unit_expression 8 percent_type_term_id Percent Type int 4 0 Y N ON_ontology_term ontology_term_id Y optionlist Y Y N percent selected cell staining level "SELECT CT.ontology_term_id,CT.term_name FROM $TBON_ONTOLOGY_TERM PT INNER JOIN $TBON_ONTOLOGY O ON ( PT.ontology_id = O.ontology_id ) INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R ON ( PT.ontology_term_id = R.subject_term_id ) INNER JOIN $TBON_ONTOLOGY_TERM CT ON ( R.object_term_id = CT.ontology_term_id) WHERE O.ontology_tag = 'SBEAMSOntology' AND PT.term_name = 'percenttype' AND CT.record_status != 'D' ORDER BY CT.sort_order,CT.term_name" IS_assay_unit_expression 9 expression_pattern_term_id Expression Pattern int 4 0 Y N ON_ontology_term ontology_term_id N optionlist Y Y N Expression pattern of this cell type IS_assay_unit_expression 10 abundance_level_id Abundance Level int 4 0 Y N IS_abundance_level abundance_level_id N optionlist Y Y N Abundance level of cell type "SELECT CT.ontology_term_id,CT.term_name FROM $TBON_ONTOLOGY_TERM PT INNER JOIN $TBON_ONTOLOGY O ON ( PT.ontology_id = O.ontology_id ) INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R ON ( PT.ontology_term_id = R.subject_term_id ) INNER JOIN $TBON_ONTOLOGY_TERM CT ON ( R.object_term_id = CT.ontology_term_id) WHERE O.ontology_tag = 'SBEAMSOntology' AND PT.term_name = 'expressionpattern' AND CT.record_status != 'D' ORDER BY CT.sort_order,CT.term_name" IS_assay_unit_expression 11 structural_unit_percent Percent Abundance of this Unit real 4 0 Y N N text 40 Y Y N A value between 0 and 100 that approximates the percentage of cells of this type in this section IS_assay_unit_expression 12 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_assay_unit_expression 13 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_unit_expression 14 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_assay_unit_expression 15 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_unit_expression 16 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_assay_unit_expression 17 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_assay_unit_expression 18 record_status Record Status char 1 0 N N N N N IS_assay 1 assay_id Assay ID int 4 0 N Y N N pkDEFAULT IS_assay 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y Y Project under which this specimen is organized "SELECT project_id,username+' - '+name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.project_id IN ( $accessible_project_ids ) AND P.record_status != 'D' ORDER BY username,name" IS_assay 3 specimen_block_id Specimen Block int 4 0 N N IS_specimen_block specimen_block_id Y optionlist Y Y N Specimen block from which the sample on this slide was prepared "SELECT specimen_block_id, specimen_block_name FROM $TBIS_SPECIMEN_BLOCK ORDER BY specimen_block_name" IS_assay 4 assay_type_term_id Assay Type int 4 0 Y N ON_ontology_term ontology_term_id N optionlist Y Y N Stain type IS_assay 5 assay_name Assay Name varchar 50 0 N N Y text 40 Y Y Y Unique name for this stain. Naming Convention: Antibody/Probe [space] specimen_block [space] section (e.g. CD90 03-123D 1). Section number default is 1. IS_assay 6 assay_description Assay Description varchar 255 0 Y N N textarea 4 Y Y N Longer description of this stain IS_assay 7 section_index Section Index varchar 50 0 Y N N text 4 Y Y N "Index of the section used for this stain (1,2,3,?)" IS_assay 8 preparation_date Preparation Date datetime 8 0 Y CURRENT_TIMESTAMP N N textdate 20 Y Y N Date this stained slide was prepared IS_assay 9 protocol_id Preparation Protocol int 4 0 N N protocol protocol_id Y optionlist Y Y Y Protocol used to prepare and stain this slide "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE PT.name='Immunostain Slide Preparation' AND P.record_status != 'D' ORDER BY P.name" IS_assay 10 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 6 Y Y N Describe any deviations from the intented above protocol to the way this preparation was actually executed IS_assay 11 cancer_amount_cc Amount of Cancer real 4 0 Y N N text 20 Y Y N Amount of cancer (in cc) present in the section IS_assay 12 contact_id Contact ID int 4 0 Y N contact contact_id N text 40 Y N N Person analyzing this slide IS_assay 13 is_control Is Control Assay char 1 0 Y N Y optionlist Y Y N Is this Stain a control Stain? "SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type='yesno' ORDER BY sort_order,option_value" IS_assay 14 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_assay 15 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_assay 16 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay 17 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_assay 18 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay 19 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_assay 20 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_assay 21 record_status Record Status char 1 0 N N N N N IS_assay_channel 1 assay_channel_id Assay Channel ID int 4 0 N Y N N pkDEFAULT IS_assay_channel 2 assay_id Assay int 4 0 N N IS_assay assay_id Y optionlist Y Y N Stain used for this sample "SELECT assay_id, assay_name FROM $TBIS_ASSAY ORDER BY assay_name" IS_assay_channel 3 channel_index Channel Index int 4 0 N N N text 4 Y Y N "Index of the section used for this stain (1,2,3,?)" IS_assay_channel 4 antibody_id Antibody int 4 0 Y N IS_antibody antibody_id N optionlist Y Y N Antibody used to stain this sample "SELECT antibody_id, antibody_name FROM $TBIS_ANTIBODY ORDER BY sort_order,antibody_name" IS_assay_channel 5 probe_id Probe int 4 0 Y N IS_probe probe_id N optionlist Y Y N Probe used to stain this sample "SELECT probe_id, probe_name FROM $TBIS_PROBE ORDER BY sort_order,probe_name" IS_assay_channel 6 detection_method_id Detection Method int 4 0 N N IS_detection_method detection_method_id N text 40 Y Y N Detection Method used to analyze this stain IS_assay_channel 7 assay_channel_name Assay Channel Name varchar 255 0 Y N Y text 40 Y Y Y Name of this channel assay. Naming convention: AssayName[space] - chan [space] assay_channel_index (e.g. CD10 01-021A 1 - chan 1) "SELECT tissue_type_id, tissue_type_name FROM $TBIS_TISSUE_TYPE ORDER BY sort_order,tissue_type_name" IS_assay_channel 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_assay_channel 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_channel 10 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_assay_channel 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_channel 12 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_assay_channel 13 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_assay_channel 14 record_status Record Status char 1 0 N N N N N IS_detection_method 1 detection_method_id Detection Method ID int 4 0 N Y N N pkDEFAULT IS_detection_method 2 detection_method_name Detection Method Name varchar 50 0 N N Y text 40 Y Y Y Name of this Detection Method IS_detection_method 3 detection_method_description Detection Method Description text 16 0 N N Y text 50 Y Y N Longer description of this Detection Method IS_detection_method 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_detection_method 5 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_detection_method 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_detection_method 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_detection_method 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_detection_method 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_detection_method 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_detection_method 11 record_status Record Status char 1 0 N N N N N IS_assay_image 1 assay_image_id Assay Image ID int 4 0 N Y N N pkDEFAULT IS_assay_image 2 assay_channel_id Assay Channel int 4 0 Y N IS_assay_channel assay_channel_id Y optionlist Y Y N Assay channel of which this is an image (or of a part of thereof) "SELECT assay_channel_id, assay_channel_name from $TBIS_ASSAY_CHANNEL ac join $TBIS_ASSAY a on ac.assay_id = a.assay_id order by antibody_id" IS_assay_image 3 parent_assay_image_id Parent Image int 4 0 Y N IS_assay_image assay_image_id N optionlist Y Y N Parent image of this image IS_assay_image 4 image_type_term_id Image Type int 4 0 Y N ON_ontology_term ontology_term_id Y optionlist Y Y N Image type ---(ONTOLOGY) "SELECT CT.ontology_term_id,CT.term_name FROM $TBON_ONTOLOGY_TERM PT INNER JOIN $TBON_ONTOLOGY O ON ( PT.ontology_id = O.ontology_id ) INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R ON ( PT.ontology_term_id = R.subject_term_id ) INNER JOIN $TBON_ONTOLOGY_TERM CT ON ( R.object_term_id = CT.ontology_term_id) WHERE O.ontology_tag = 'SBEAMSOntology' AND PT.term_name = 'assayimagetype' AND CT.record_status != 'D' ORDER BY CT.sort_order,CT.term_name" IS_assay_image 5 image_name Image Name varchar 255 0 N N Y text 20 Y Y Y "Name of image file, should convey sample information in accordance with established naming convention" IS_assay_image 6 image_description Image Description text 16 0 Y N N text 50 Y Y N Longer description for this image IS_assay_image 7 image_magnification Image Magnification real 4 0 N N Y text 20 Y Y N Magnification of the instrument for this image (Enter a decimal number with no 'x' or other characters) IS_assay_image 8 protocol_id Imaging Protocol int 4 0 N N protocol protocol_id Y optionlist Y Y N Protocol used to image this assay channel "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE PT.name='Immunostain Image Acquisition' AND P.record_status != 'D' ORDER BY P.name" IS_assay_image 9 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 6 Y Y N Describe any deviations from the intented above protocol to the way this slide was actually imaged or supply special instrument settings not normally recorded in the protocol IS_assay_image 10 image_file_date Image Date datetime 8 0 Y CURRENT_TIMESTAMP N N textdate 20 Y Y N Date this image was taken IS_assay_image 11 raw_image_file Raw Image File varchar 255 0 Y N N file 40 Y Y N Click BROWSE and select the raw image file to be uploaded via the web interface uploaded_file IS_assay_image 12 processed_image_file Processed Image File varchar 255 0 Y N N file 40 Y Y N "Click BROWSE and select the processed image file (e.g., contrast adjustment or other enhancements in Photoshop) to be uploaded via the web interface" uploaded_file IS_assay_image 13 annotated_image_file Annotated Image File varchar 255 0 Y N N file 40 Y Y N "Click BROWSE and select the annotated image file (e.g., with labels or markers indicating interesting features) to be uploaded via the web interface" uploaded_file IS_assay_image 14 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_assay_image 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_image 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_assay_image 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_image 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_assay_image 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_assay_image 20 record_status Record Status char 1 0 N N N N N IS_assay_image_subfield 1 assay_image_subfield_id Assay Image Subfield ID int 4 0 N Y N N pkDEFAULT IS_assay_image_subfield 2 assay_image_id Containing Image int 4 0 Y N IS_assay_image assay_image_id Y optionlist Y Y N Image of which this is a subfield (or of a part of thereof) "SELECT assay_image_id, image_name FROM $TBIS_ASSAY_IMAGE ORDER BY image_name" IS_assay_image_subfield 3 subfield_name Subfield Name varchar 255 0 N N Y text 20 Y Y Y Name of image subfield IS_assay_image_subfield 4 subfield_boundaries Subfield Boundaries varchar 255 0 N N Y text 20 Y Y Y Designation of subfield boundaries IS_assay_image_subfield 5 subfield_description Subfield Description text 16 0 N N Y text 50 Y Y N Longer description of this image subfield IS_assay_image_subfield 6 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_assay_image_subfield 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_image_subfield 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_assay_image_subfield 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_assay_image_subfield 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_assay_image_subfield 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_assay_image_subfield 12 record_status Record Status char 1 0 N N N N N IS_tissue_type 1 tissue_type_id Tissue Type ID int 4 0 N Y N N pkDEFAULT IS_tissue_type 2 tissue_type_name Tissue Type Name varchar 50 0 N N Y text 40 Y Y Y Name of this Tissue Type IS_tissue_type 3 tissue_type_description Tissue Type Description varchar 255 0 N N Y text 50 Y Y N Longer description of this Tissue Type IS_tissue_type 4 is_cancerous Is Cancerous char 1 0 N N Y optionlist Y Y N Is this tissue type a cancerous type? "SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type='yesno' ORDER BY sort_order,option_value" IS_tissue_type 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_tissue_type 6 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Integer designed to assist in sort records of this type IS_tissue_type 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_tissue_type 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_tissue_type 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_tissue_type 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_tissue_type 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_tissue_type 12 record_status Record Status char 1 0 N N N N N IS_specimen 1 specimen_id Specimen int 4 0 N Y N N pkDEFAULT IS_specimen 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y N Project under which this specimen is organized "SELECT project_id,username+' - '+name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.project_id IN ( $accessible_project_ids ) AND P.record_status != 'D' ORDER BY username,name" IS_specimen 3 specimen_name Specimen Name/Designator varchar 50 0 N N Y text 40 Y Y Y Name/Coded designator for this specimen IS_specimen 4 organism_id Organism int 4 0 Y N organism organism_id Y optionlist Y Y N Organism (genus+species) name of the individual from which this specimen was harvested "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" IS_specimen 5 tissue_type_id Tissue Type int 4 0 N N IS_tissue_type tissue_type_id Y optionlist Y Y N Tissue type of this specimen "SELECT tissue_type_id, tissue_type_name FROM $TBIS_TISSUE_TYPE ORDER BY sort_order,tissue_type_name" IS_specimen 6 individual_age Individual Age real 4 0 Y N N text 20 Y Y N Age in years of specimen donor IS_specimen 7 individual_sex_term_id Individual Sex int 4 0 Y N ON_ontology_term ontology_term_id N optionlist 20 Y Y N "Sex of donor (m = male, f = female) " "SELECT CT.ontology_term_id,CT.term_name FROM $TBON_ONTOLOGY_TERM PT INNER JOIN $TBON_ONTOLOGY O ON ( PT.ontology_id = O.ontology_id ) INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R ON ( PT.ontology_term_id = R.subject_term_id ) INNER JOIN $TBON_ONTOLOGY_TERM CT ON ( R.object_term_id = CT.ontology_term_id) WHERE O.ontology_tag = 'SBEAMSOntology' AND PT.term_name = 'sex' AND CT.record_status != 'D' ORDER BY CT.sort_order,CT.term_name" IS_specimen 8 surgical_procedure_term_id Surgical Procedure int 4 0 Y N ON_ontology_term ontology_term_id N optionlist Y Y N Surgical Procedure used to obtain this specimen ---(ONTOLOGY) "SELECT CT.ontology_term_id,CT.term_name FROM $TBON_ONTOLOGY_TERM PT INNER JOIN $TBON_ONTOLOGY O ON ( PT.ontology_id = O.ontology_id ) INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R ON ( PT.ontology_term_id = R.subject_term_id ) INNER JOIN $TBON_ONTOLOGY_TERM CT ON ( R.object_term_id = CT.ontology_term_id) WHERE O.ontology_tag = 'SBEAMSOntology' AND PT.term_name = 'surgicalprocedure' AND CT.record_status != 'D' ORDER BY CT.sort_order,CT.term_name" IS_specimen 9 clinical_diagnosis_term_id Clinical Diagnosis int 4 0 Y N ON_ontology_term ontology_term_id N optionlist Y Y N Clinical Diagnosis of donor "SELECT CT.ontology_term_id,CT.term_name FROM $TBON_ONTOLOGY_TERM PT INNER JOIN $TBON_ONTOLOGY O ON ( PT.ontology_id = O.ontology_id ) INNER JOIN $TBON_ONTOLOGY_TERM_RELATIONSHIP R ON ( PT.ontology_term_id = R.subject_term_id ) INNER JOIN $TBON_ONTOLOGY_TERM CT ON ( R.object_term_id = CT.ontology_term_id) WHERE O.ontology_tag = 'SBEAMSOntology' AND PT.term_name = 'ClinicalDiagnosis' AND CT.record_status != 'D' ORDER BY CT.sort_order,CT.term_name" IS_specimen 10 protocol_id Preparation Protocol int 4 0 N N protocol protocol_id Y optionlist Y Y Y Protocol used to prepare this specimen "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE PT.name='Immunostain Slide Preparation' AND P.record_status != 'D' ORDER BY P.name" IS_specimen 11 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 6 Y Y N Describe any deviations from the intented above protocol to the way this preparation was actually executed IS_specimen 12 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_specimen 13 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_specimen 14 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_specimen 15 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_specimen 16 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_specimen 17 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_specimen 18 record_status Record Status char 1 0 N N N N N IS_specimen_block 1 specimen_block_id Specimen Block int 4 0 N Y N N pkDEFAULT IS_specimen_block 2 specimen_block_name Specimen Block Name/Designator varchar 50 0 N N Y text 40 Y Y Y Name/Coded designator for this specimen block IS_specimen_block 3 specimen_id Specimen int 4 0 N N IS_specimen specimen_id Y optionlist Y Y N Specimen from which this block was taken "SELECT specimen_id, specimen_name FROM $TBIS_SPECIMEN ORDER BY specimen_name" IS_specimen_block 4 protocol_id Preparation Protocol int 4 0 N N protocol protocol_id Y optionlist Y Y N Protocol used to prepare this specimen block "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE PT.name='Immunostain Specimen Preparation' AND P.record_status != 'D' ORDER BY P.name" IS_specimen_block 5 acquisition_time Acquisition Time real 4 0 Y N N text 20 Y Y N Time in minutes between harvesting specimen and fixing specimen block IS_specimen_block 6 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 6 Y Y N Describe any deviations from the intented above protocol to the way this preparation was actually executed IS_specimen_block 7 specimen_block_level Specimen Block Level varchar 50 0 Y N N text 20 Y Y N Level designator for the specimen block IS_specimen_block 8 anterior_posterior Anterior or Posterior varchar 50 0 Y N N text 40 Y Y N Anterior or Posterior designation for the specimen block IS_specimen_block 9 specimen_block_side Specimen Block Side varchar 50 0 Y N N text 40 Y Y N Left/right side of the individual from this specimen block IS_specimen_block 10 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments IS_specimen_block 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N IS_specimen_block 12 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N IS_specimen_block 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N IS_specimen_block 14 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N IS_specimen_block 15 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N IS_specimen_block 16 record_status Record Status char 1 0 N N N N N IS_SummarizeStains 1 project_id Projects N multioptionlist 4 Y Y N Constrain query to selected projects. Multiple projects may be selected. "SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P INNER JOIN $TBIS_ASSAY SS ON ( P.project_id = SS.project_id ) LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' ORDER BY UL.username+' - '+P.name,P.project_id" IS_SummarizeStains 2 organism_id Organism N multioptionlist 4 Y Y N Constrain query to selected organism. Multiple organisms may be selected. "SELECT DISTINCT sbo.organism_id, sbo.organism_name from $TBIS_SPECIMEN S join sbeams.dbo.organism sbo on S.organism_id = sbo.organism_id WHERE S.record_status != 'D' " IS_SummarizeStains 3 specimen_block_id Specimen Blocks N multioptionlist 4 Y Y N Constrain query only to selected specimen blocks Multiple specimen blocks may be selected. "SELECT DISTINCT SB.specimen_block_id,SB.specimen_block_name FROM $TBIS_SPECIMEN_BLOCK SB INNER JOIN $TBIS_ASSAY SS ON ( SB.specimen_block_id = SS.specimen_block_id ) WHERE SS.record_status != 'D' ORDER BY SB.specimen_block_name" IS_SummarizeStains 4 weighting_factor Weighting Factor N text 7 Y Y N Weighting value given to equivocal staining for compiling staining summary. Must be between 0 and 1 IS_SummarizeStains 5 genome_coordinates_constraint Genome Coordinates N text 50 Y Y N Specify the antibodies to constraint the query with using genome coordinates in a form like hg16:chr5:123456-123457+ where hg16 is the build and the final character is the orientation + or - IS_SummarizeStains 6 antibody_id Antibodies N multioptionlist 4 Y Y N Constrain query only to selected antibodies Multiple antibodies may be selected. "SELECT DISTINCT AB.antibody_id,AB.antibody_name,AB.sort_order FROM $TBIS_ANTIBODY AB INNER JOIN $TBIS_ASSAY_CHANNEL AC ON ( AB.antibody_id = AC.antibody_id ) WHERE AC.record_status != 'D' ORDER BY AB.sort_order, AB.antibody_name" IS_SummarizeStains 7 probe_id Probes N multioptionlist 4 Y Y N Constrain query only to selected probe. Multiple probes may be selected. "SELECT DISTINCT P.probe_id,P.probe_name,P.sort_order FROM $TBIS_PROBE P INNER JOIN $TBIS_ASSAY_CHANNEL AC ON ( P.probe_id = AC.probe_id ) WHERE AC.record_status != 'D' ORDER BY P.sort_order,P.probe_name" IS_SummarizeStains 8 tissue_type_id Tissue Type N multioptionlist 4 Y Y N Constrain query to selected tissue types. Multiple tissue types may be selected. "SELECT DISTINCT TT.tissue_type_id,TT.tissue_type_name,TT.sort_order FROM $TBIS_TISSUE_TYPE TT INNER JOIN $TBIS_SPECIMEN S ON ( TT.tissue_type_id = S.tissue_type_id ) WHERE S.record_status != 'D' ORDER BY TT.sort_order,TT.tissue_type_name" IS_SummarizeStains 9 structural_unit_id Structural Unit N multioptionlist 4 Y Y N Constrain query only to selected structural units Multiple structural units may be selected. "SELECT structural_unit_id,structural_unit_name,sort_order FROM $TBIS_STRUCTURAL_UNIT WHERE record_status !='D' ORDER BY sort_order,structural_unit_name" IS_SummarizeStains 10 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBIS_QUERY_OPTION WHERE option_type = 'SS_display_options' ORDER BY sort_order,option_value" IS_genome_coordinates 1 genome_coordinates_id Gene Coordinates ID int 4 Y N N pkDEFAULT IS_genome_coordinates 2 refseq_id RefSeq ID varchar 50 N Y Y Y IS_genome_coordinates 3 locus_link_id LocusLink ID int 4 N Y Y Y IS_genome_coordinates 4 genome_chromosome Chromosome varchar 50 N Y Y IS_genome_coordinates 5 genome_strand DNA Strand varchar 2 N Y Y IS_genome_coordinates 6 genome_transcription_start Gene Transcription Start int 4 N Y Y IS_genome_coordinates 7 genome_transcription_end Gene Transcription End int 4 N Y Y IS_genome_coordinates 8 genome_coding_region_start Gene Coding Start int 4 N Y Y IS_genome_coordinates 9 genome_coding_region_end Gene Coding End int 4 N Y Y IS_genome_coordinates 10 genome_location Chromosomal Location varchar 255 N Y Y IS_genome_coordinates 11 organism_id Organism int 4 N Y Y IS_genome_coordinates 12 comment Comment text 16 N N N IS_genome_coordinates 13 date_created Date Record Created datetime 16 CURRENT N Y N N IS_genome_coordinates 14 created_by_id Record Created By int 4 1 N contact contact_id Y N N IS_genome_coordinates 15 date_modified Date Record Modified datetime 16 CURRENT N Y N N IS_genome_coordinates 16 modified_by_id Record Modified By int 4 1 N contact contact_id Y N N IS_genome_coordinates 17 owner_group_id Owner Group ID int 4 1 N work_group work_group_id Y N N IS_genome_coordinates 18 record_status Record Status char 1 N N N N