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
MA_slide_type 1 slide_type_id Slide Type ID int 8 0 N Y N N pkDEFAULT
MA_slide_type 2 name Name varchar 50 0 N N Y text 50 Y Y Y Short name of this slide type
MA_slide_type 3 organism_id Organism int 8 0 N N organism_id Y optionlist Y Y N Organism for this type "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"
MA_slide_type 4 price Price float 8 0 Y N N text 25 Y Y N Arrays Lab price for this slide_type
MA_slide_type 5 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_slide_type 6 sort_order Sort Order int 4 0 N 10 N N N N
MA_slide_type 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_type 8 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_slide_type 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_type 10 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_slide_type 11 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_slide_type 12 record_status Record Status char 1 0 N N N N N
MA_cost_scheme 1 cost_scheme_id Cost Scheme ID int 8 0 N Y N N pkDEFAULT
MA_cost_scheme 2 cost_scheme_name Scheme Name varchar 50 0 N N Y text 50 Y Y Y Short name of this cost scheme
MA_cost_scheme 3 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_cost_scheme 4 sort_order Sort Order int 4 0 N 10 N N N N
MA_cost_scheme 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_cost_scheme 6 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_cost_scheme 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_cost_scheme 8 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_cost_scheme 9 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_cost_scheme 10 record_status Record Status char 1 0 N N N N N
MA_slide_type_cost 1 slide_type_cost_id Slide Type ID int 8 0 N Y N N pkDEFAULT
MA_slide_type_cost 2 slide_type_id Slide Type int 8 0 N N MA_slide_type slide_type_id Y optionlist Y Y Y Slide Type for this price "SELECT slide_type_id, name FROM $TBMA_SLIDE_TYPE ORDER BY sort_order,name"
MA_slide_type_cost 3 cost_scheme_id Cost Scheme int 8 0 N N MA_cost_scheme cost_scheme_id Y optionlist Y Y Y Cost Scheme for this price "SELECT cost_scheme_id, cost_scheme_name FROM $TBMA_COST_SCHEME ORDER BY sort_order,cost_scheme_name"
MA_slide_type_cost 4 price Price float 8 0 Y N Y text 25 Y Y N Arrays Lab price for this slide_type
MA_slide_type_cost 5 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_slide_type_cost 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_type_cost 7 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_slide_type_cost 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_type_cost 9 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_slide_type_cost 10 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_slide_type_cost 11 record_status Record Status char 1 0 N N N N N
MA_labeling_method 1 labeling_method_id Labeling Method ID int 8 0 N Y N N pkDEFAULT
MA_labeling_method 2 name Method Name varchar 100 0 N N Y text 50 Y Y Y Name of this labeling method
MA_labeling_method 3 xna_type_id xNA Type int 8 0 N N xna_type_id Y optionlist Y Y Y xNA type "SELECT xna_type_id, xna_type FROM $TBMA_XNA_TYPE ORDER BY sort_order,xna_type"
MA_labeling_method 4 dye_id Dye int 8 0 N N dye_id Y optionlist Y Y Y Dye "SELECT dye_id, dye_name FROM $TBMA_DYE ORDER BY dye_name"
MA_labeling_method 5 desired_micrograms Desired Micrograms float 8 0 Y N N text 25 Y Y N Number of micrograms required to label
MA_labeling_method 6 Ebase Ebase float 8 0 Y N Y text 25 Y Y N Extinction coefficient for a base
MA_labeling_method 7 MWbase MWbase float 8 0 Y N Y text 25 Y Y N Molecular weight for a base in g/mol
MA_labeling_method 8 price Price float 8 0 Y N N text 25 Y Y N Arrays Lab price for this labeling method
MA_labeling_method 9 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional notes
MA_labeling_method 10 sort_order Sort Order int 4 0 N 10 N N N N
MA_labeling_method 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_labeling_method 12 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_labeling_method 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_labeling_method 14 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_labeling_method 15 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_labeling_method 16 record_status Record Status char 1 0 N N N N N
MA_array_request 1 array_request_id Array Request ID int 8 0 N Y N N pkDEFAULT
MA_array_request 2 contact_id Contact int 8 0 N N contact contact_id Y current_contact_id Y Y N Requestor of these slides
MA_array_request 3 project_id Project int 8 0 N N project project_id Y optionlist Y Y N Project under which these slides are requested "SELECT project_id, name || ' ['||budget||']' FROM $TB_PROJECT WHERE PI_contact_id='$contact_id' AND record_status != 'D' ORDER BY name"
MA_array_request 4 cost_scheme_id Cost Structure varchar 50 0 N N N optionlist Y Y N Cost Structure from which pricing is calculated "SELECT cost_scheme_id,cost_scheme_name FROM $TBMA_COST_SCHEME ORDER BY sort_order,cost_scheme_name"
MA_array_request 5 slide_type_id Slide Type int 8 0 N N MA_slide_type slide_type_id Y optionlist Y Y N Slide Type MANUAL
MA_array_request 6 n_slides Number of Arrays int 8 0 N N Y text 10 Y Y N "Number of arrays in this request (note that for the Yeast Half slide option, the number of arrays you specify here is TWICE the number of pieces of glass)"
MA_array_request 7 n_samples_per_slide Samples per Array int 8 0 N N Y optionlist Y Y N Number of samples per array (usually 2) "SELECT option_key,option_value FROM $TBMA_MISC_OPTION WHERE option_type='samples_per_slide' ORDER BY sort_order,option_value"
MA_array_request 8 hybridization_request Prep Request varchar 50 0 N N Y optionlist Y Y N Whether you want the arrays Group to perform labeling and hybridization (priced by labeling method) "SELECT option_key,option_value FROM $TBMA_ARRAY_REQUEST_OPTION WHERE option_type='hybridization_request' ORDER BY sort_order,option_value"
MA_array_request 9 scanning_request Analysis Request varchar 50 0 N N Y optionlist Y Y N Whether you want the arrays Group to perform Scanning and Quantitation "SELECT option_key,option_value||' (\$'||CONVERT(varchar(50),price)||')' FROM $TBMA_ARRAY_REQUEST_OPTION WHERE option_type='scanning_request' ORDER BY sort_order,option_value"
MA_array_request 10 request_status Request Status varchar 50 0 N N Y fixed Y Y N Status of this request "SELECT option_key,option_value FROM $TBMA_MISC_OPTION WHERE option_type='job_status' ORDER BY sort_order,option_value"
MA_array_request 11 price Price int 8 0 Y N N fixed N Y N Total price for this request
MA_array_request 12 comment Comment text 0 0 Y N N textarea 4 Y Y N Additional comments about this request
MA_array_request 13 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N fixed N Y
MA_array_request 14 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_array_request 15 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N fixed N Y
MA_array_request 16 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_array_request 17 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_array_request 18 record_status Record Status char 1 0 N N N fixed N Y
MA_array_request_slide 1 array_request_slide_id Array Request Slide ID int 4 0 N Y Y N N pkDEFAULT
MA_array_request_slide 2 array_request_id Array Request ID int 4 0 N N MA_array_request array_request_id Y optionlist Y Y Y Array request to which this requested slide belongs
MA_array_request_slide 3 slide_index Slide Index int 4 0 N N Y text 10 Y Y Y "Index of this slide within the request (1,2,3,4,etc.)"
MA_array_request_slide 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N Y
MA_array_request_slide 5 created_by_id Record Created By int 4 0 N N contact contact_id N N
MA_array_request_slide 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_request_slide 7 modified_by_id Record Modified By int 4 0 N N contact contact_id N N
MA_array_request_slide 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_array_request_slide 9 record_status Record Status char 1 0 N N N N N
MA_array_request_sample 1 array_request_sample_id Array Request Sample ID int 4 0 N Y Y N N pkDEFAULT
MA_array_request_sample 2 array_request_slide_id Array Request Slide ID int 4 0 N N MA_array_request_MA_slide array_request_slide_id Y fixed N Y Y Array request slide to which this sample belongs pkDEFAULT
MA_array_request_sample 3 sample_index Sample Index int 4 0 N N Y fixed N Y Y "Index of this sample on the slide (1,2,3,4,etc.)"
MA_array_request_sample 4 name Sample Name varchar 50 0 N N Y text 50 Y Y N Sample Name. Keep it short. Do not use any strange characters like /\*&$() (e.g. NP Epi 03-123)
MA_array_request_sample 5 full_name Full Name varchar 255 0 N N Y textarea 3 Y Y N "Full Sample Name. A longer, less cryptic name should be placed here. It should be long enough so that someone else can understand quickly the general idea of the sample. (e.g. Epithelial cells FACS sorted from ""normal"" prostate tissue from specimen 03-123)"
MA_array_request_sample 6 labeling_method_id Labeling Method int 4 0 N N MA_labeling_method labeling_method_id Y fixed N N N Labeling method requested for this sample. Not necessarily what was actually done?
MA_array_request_sample 7 sample_provider_organization_id Sample Provider int 4 0 Y N organization organization_id N optionlist Y Y N "Provider of this biomaterial (academic department, research lab, vendor, etc.)" "SELECT O.organization_id,O.organization FROM $TB_ORGANIZATION O INNER JOIN $TB_ORGANIZATION_TYPE OT ON (O.organization_type_id=OT.organization_type_id) WHERE O.record_status != 'D' ORDER BY organization"
MA_array_request_sample 8 organism_id Organism int 4 0 Y N organism organism_id N optionlist Y Y N Organism from which the biomaterial was derived "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"
MA_array_request_sample 9 strain_or_line Strain or Line varchar 255 0 Y N N text 50 Y Y N Strain or line of the individual
MA_array_request_sample 10 individual Individual varchar 255 0 Y N N text 50 Y Y N Identifier or name of the individual organism from which the biomaterial was derived
MA_array_request_sample 11 sex_ontology_term_id Sex int 4 0 Y N N optionlist Y Y N Sex of the individual MANUAL
MA_array_request_sample 12 age Age varchar 255 0 Y N N text 50 Y Y N "Age of the individual at the time of harvest of the biomaterial. Free form text; include units, developmental stage, and reference point as appropriate (e.g., days since planting, years after birth, minutes after death)"
MA_array_request_sample 13 organism_part Organism Part varchar 255 0 Y N N text 50 Y Y N "Part of the organism's anatomy from the biomaterial was derived, excludes cells. (e.g., tissue, organ, system, or body location)"
MA_array_request_sample 14 cell_line Cell Line varchar 255 0 Y N N text 50 Y Y N Identifier for the cell line if one was used as a biomaterial
MA_array_request_sample 15 cell_type Cell Type varchar 255 0 Y N N text 50 Y Y N "Type of cell used as the biomaterial (e.g., epithelial, glial, etc.)"
MA_array_request_sample 16 disease_state Disease State varchar 255 0 Y N N text 50 Y Y N "Name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is ""normal"" if no disease state has been diagnosed."
MA_array_request_sample 17 protocol_ids Protocols varchar 255 0 Y N MA_sample_protocol sample_protocol_id N multilink 4 Y Y N Select all protocols that apply to this biomaterial. Describe sequence of protocols in the Treatment Description below "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 P.record_status != 'D' ORDER BY P.name"
MA_array_request_sample 18 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 4 Y Y N Describe any deviations from the selected protocols
MA_array_request_sample 19 sample_description Sample Description text 16 0 Y N N textarea 4 Y Y N Describe the biomaterial briefly
MA_array_request_sample 20 sample_preparation_date Sample Preparation Date datetime 8 0 N N N text 30 Y Y Y Date/time the biomaterial was prepared with the described protocols
MA_array_request_sample 21 treatment_description Treatment Description text 16 0 Y N N textarea 4 Y Y N "Describe the treatment of the biomaterials, including mention of the selected protocols"
MA_array_request_sample 22 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional notes
MA_array_request_sample 23 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N Y
MA_array_request_sample 24 created_by_id Record Created By int 4 0 N N contact contact_id N N
MA_array_request_sample 25 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_request_sample 26 modified_by_id Record Modified By int 4 0 N N contact contact_id N N
MA_array_request_sample 27 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_array_request_sample 28 record_status Record Status char 1 0 N N N N N
MA_sample_protocol 1 sample_protocol_id Sample Protocol int 4 0 N Y N N N
MA_sample_protocol 2 array_request_sample_id Array Request Sample ID int 4 0 N N MA_array_request_sample array_request_sample_id Y N N Y Array request sample ID
MA_sample_protocol 3 protocol_id Protocol ID int 4 0 N N protocol protocol_id Y N N Y Protocol ID
MA_sample_protocol 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_sample_protocol 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N
MA_sample_protocol 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_sample_protocol 7 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N
MA_sample_protocol 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_sample_protocol 9 record_status Record Status char 1 0 N N N N N
MA_slide_model 1 slide_model_id Slide Model ID int 8 0 N Y N N pkDEFAULT
MA_slide_model 2 vendor_name Vendor Name varchar 50 0 N N Y text 50 Y Y Y Vendor for this slide model
MA_slide_model 3 model_name Model Name varchar 50 0 N N Y text 50 Y Y Y Model name of these slides
MA_slide_model 4 contact_id Contact int 8 0 N N contact contact_id Y optionlist Y Y Y Vendor contact entry for these slides "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"
MA_slide_model 5 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_slide_model 6 sort_order Sort Order int 4 0 N 10 N N N N
MA_slide_model 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_model 8 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_slide_model 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_model 10 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_slide_model 11 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_slide_model 12 record_status Record Status char 1 0 N N N N N
MA_slide_lot 1 slide_lot_id Slide Lot ID int 8 0 N Y N N pkDEFAULT
MA_slide_lot 2 slide_model_id Slide Model int 8 0 N N MA_slide_model slide_model_id Y optionlist Y Y Y Model name of these slides "SELECT slide_model_id,vendor_name||' '||model_name AS 'name' FROM $TBMA_SLIDE_MODEL ORDER BY 2"
MA_slide_lot 3 lot_number Lot Number varchar 50 0 N N Y text 50 Y Y Y Lot number of these slides
MA_slide_lot 4 date_received Date Received datetime 8 0 Y N N textdate 30 Y Y N Date this lot was received
MA_slide_lot 5 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_slide_lot 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_lot 7 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_slide_lot 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide_lot 9 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_slide_lot 10 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_slide_lot 11 record_status Record Status char 1 0 N N N N N
MA_printing_batch 1 printing_batch_id Printing Batch ID int 8 0 N Y N N pkDEFAULT
MA_printing_batch 2 slide_type_id Slide Type int 8 0 N N MA_slide_type slide_type_id Y optionlist Y Y Y Slide type "SELECT slide_type_id, name FROM $TBMA_SLIDE_TYPE ORDER BY sort_order,name"
MA_printing_batch 3 protocol_id Protocol int 8 0 N N protocol protocol_id Y optionlist Y Y Y Protocol for this printing "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='array_printing' AND P.record_status != 'D' ORDER BY P.name"
MA_printing_batch 4 date_started Date Started datetime 8 0 N N Y text 30 Y Y Y Date/time the printing began
MA_printing_batch 5 date_finished Date Finished datetime 8 0 Y N N text 30 Y Y N Date/time the printing finished
MA_printing_batch 6 number_of_spots Number of Spots int 4 0 Y N N text 10 Y Y N Number of spots per slide
MA_printing_batch 7 spot_spacing Spot Spacing (microns) float 8 0 N N Y text 10 Y Y N Spacing of the spots
MA_printing_batch 8 solvent Solvent varchar 50 0 N N Y optionlist Y Y N Solvent used "SELECT option_key,option_value FROM $TBMA_MISC_OPTION WHERE option_type='solvent' ORDER BY sort_order,option_value"
MA_printing_batch 9 temperature Temperature float 8 0 Y N N text 10 Y Y N Temperature during printing
MA_printing_batch 10 humidity Humidity float 8 0 Y N N text 10 Y Y N Humidity during printing
MA_printing_batch 11 post_treatment Post Treatment varchar 50 0 N N Y optionlist Y Y N Post treatment of slides "SELECT option_key,option_value FROM $TBMA_MISC_OPTION WHERE option_type='post_treatment' ORDER BY sort_order,option_value"
MA_printing_batch 12 slide_list Slide List varchar 255 0 Y N N text 50 Y Y N Serial numbers of slides printed (NOTE: this is a non-binding entry; it does not automatically create slides associated with this printing)
MA_printing_batch 13 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_printing_batch 14 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_printing_batch 15 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_printing_batch 16 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_printing_batch 17 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_printing_batch 18 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_printing_batch 19 record_status Record Status char 1 0 N N N N N
MA_slide 1 slide_id Slide ID int 8 0 N Y N N pkDEFAULT
MA_slide 2 slide_lot_id Slide Lot int 8 0 N N MA_slide_lot slide_lot_id Y optionlist Y Y Y Slide Lot "SELECT slide_lot_id, vendor_name||' '||model_name||' # '||lot_number FROM $TBMA_SLIDE_LOT SL LEFT JOIN $TBMA_SLIDE_MODEL SM ON (SL.slide_model_id=SM.slide_model_id) ORDER BY 2"
MA_slide 3 slide_number Slide Number int 4 0 N N Y text 10 Y Y Y "Slide Number (you may enter a range such as 50-68,70-75 to generate many entries)"
MA_slide 4 barcode Barcode varchar 50 0 Y N N text 25 Y Y Y Barcode
MA_slide 5 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_slide 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide 7 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_slide 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_slide 9 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_slide 10 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_slide 11 record_status Record Status char 1 0 N N N N N
MA_array_layout 1 layout_id Layout ID int 8 0 N Y N N pkDEFAULT
MA_array_layout 2 slide_type_id Slide Type int 8 0 N N MA_slide_type slide_type_id Y optionlist Y Y Y Slide type "SELECT slide_type_id, name FROM $TBMA_SLIDE_TYPE ORDER BY sort_order,name"
MA_array_layout 3 name name varchar 50 0 N N Y text 25 setLayoutFileName() Y Y Y Name of this layout
MA_array_layout 4 data_file Data File varchar 100 0 N N N file 50 N N N Click Browse and select the file to upload to the database
MA_array_layout 5 biosequence_set_id Biosequence Set int 8 0 N N MA_biosequence_set biosequence_set_id Y optionlist Y Y N Biosequence Set pertaining to this layout "SELECT biosequence_set_id, set_name FROM $TBMA_BIOSEQUENCE_SET ORDER BY sort_order,set_name"
MA_array_layout 6 source_filename Source Filename varchar 100 0 N N Y text 50 Y Y N Enter the network location of the key file
MA_array_layout 7 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments
MA_array_layout 8 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_layout 9 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_array_layout 10 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_layout 11 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_array_layout 12 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_array_layout 13 record_status Record Status char 1 0 N N N N N
MA_array 1 array_id Layout ID int 8 0 N Y document.forms[0].MA_array_name.value=document.forms[0].MA_slide_id.options[document.forms[0].MA_slide_id.selectedIndex].text N N pkDEFAULT
MA_array 2 project_id Project int 8 0 N N project project_id Y optionlist Y Y N Project to which this microarray is to be assigned "SELECT project_id, username||' - '||name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN US ON ( P.PI_contact_id=US.contact_id ) WHERE P.project_id IN ( $accessible_project_ids ) AND P.record_status != 'D' ORDER BY name"
MA_array 3 layout_id Layout int 8 0 N N MA_array_layout layout_id Y optionlist Y Y N Layout name associated with this microarray "SELECT layout_id, ST.name||' - '||AL.name FROM $TBMA_ARRAY_LAYOUT AL LEFT JOIN $TBMA_SLIDE_TYPE ST ON ( AL.slide_type_id=ST.slide_type_id ) ORDER BY ST.name,AL.name"
MA_array 4 printing_batch_id Printing Batch int 8 0 N N MA_printing_batch printing_batch_id Y optionlist Y Y N Printing batch in which this microarray was produced "SELECT printing_batch_id, ST.name||' ('||slide_list||') ('||SUBSTRING(CONVERT(varchar(50),date_started,121),1,16)||')' FROM $TBMA_PRINTING_BATCH PB LEFT JOIN $TBMA_SLIDE_TYPE ST ON ( PB.slide_type_id=ST.slide_type_id ) ORDER BY ST.name,date_started"
MA_array 5 slide_id Slide int 8 0 N N MA_slide slide_id Y scrolloptionlist 4 setArrayName() Y Y N Slide serial number for this microarray (choose only one slide) "SELECT S.slide_id, convert(varchar(20),slide_number)||CASE WHEN A.slide_id IS NOT NULL THEN ' - *DONE*' ELSE '' END FROM $TBMA_SLIDE S LEFT JOIN $TBMA_ARRAY A ON ( S.slide_id=A.slide_id ) ORDER BY slide_number"
MA_array 6 array_name Array Name varchar 50 0 N N Y text 25 Y Y Y "Official Name of this microarray that it will be subsequently referred to (usually just the serial number of the slide, but can be different)"
MA_array 7 array_request_slide_id Requested Slide ID int 8 0 N N array_request_slide_id Y scrolloptionlist 4 Y Y N ID assigned to this slide during the array request process MANUAL
MA_array 8 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Optional comment about this particular microarray
MA_array 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array 10 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_array 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array 12 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_array 13 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_array 14 record_status Record Status char 1 0 N N N N N
MA_labeling 1 labeling_id Labeling ID int 8 0 N Y N N pkDEFAULT
MA_labeling 2 array_request_sample_id Array Request Sample ID int 8 0 N N array_request_sample_id Y multioptionlist 4 Y Y Y "Sample ID number - Sample name (you may select several samples to enter at once, but note all values will be the same)" MANUAL
MA_labeling 3 protocol_id Protocol int 8 0 N N protocol protocol_id Y optionlist Y Y N Protocol used for labeling "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='extract_labeling' OR PT.name='Genicon Labeling' ORDER BY P.name"
MA_labeling 4 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 4 Y Y N List any deviations from the selected protocol
MA_labeling 5 spiking_controls Spiking Controls text 16 0 Y N N textarea 4 Y Y N "Describe the external controls added to the extract, including which features are expected to hybridize with control, spike type, and expected values or other parameters."
MA_labeling 6 date_labeled Date Labeled datetime 8 0 N CURRENT_TIMESTAMP N N textdate 30 Y Y N Date/time the labeling was performed
MA_labeling 7 dye_lot_number Dye Lot # varchar 25 0 Y N Y text 10 Y Y N Lot number of dye used
MA_labeling 8 absorbance_260 Absorbance at 260nm float 8 0 Y N N text 10 Y Y N Absorbance value at 260 nm
MA_labeling 9 absorbance_lambda Absorbance at dyeWL float 8 0 Y N N text 10 Y Y N Absorbance value at the reference wavelength for the dye used
MA_labeling 10 volume Volume float 8 0 Y N N text 10 Y Y N Volume in microliters (ul)
MA_labeling 11 dilution_factor Dilution Factor float 8 0 Y N N text 10 refreshDocument() Y Y N Dilutional factor
MA_labeling 12 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Additional comments about this step
MA_labeling 13 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_labeling 14 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_labeling 15 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_labeling 16 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_labeling 17 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_labeling 18 record_status Record Status char 1 0 N N N N N
MA_hybridization 1 hybridization_id Hybridization ID int 8 0 N Y N N pkDEFAULT
MA_hybridization 2 name Batch Name varchar 100 0 Y N N text 25 Y Y N Arbitrary name for this hybridization
MA_hybridization 3 protocol_id Protocol int 8 0 N N protocol protocol_id Y optionlist Y Y N Protocol used for this step "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='hybridization' ORDER BY P.name"
MA_hybridization 4 array_id Array Name int 8 0 N N MA_array array_id Y multioptionlist 4 Y Y Y Array Name (must already have been defined) "SELECT A.array_id,array_name||CASE WHEN H.array_id IS NOT NULL THEN ' - *DONE*' ELSE '' END, H.array_id FROM $TBMA_ARRAY A LEFT JOIN $TBMA_HYBRIDIZATION H ON ( A.array_id=H.array_id ) ORDER BY A.array_name"
MA_hybridization 5 date_hybridized Date Hybridized datetime 8 0 N CURRENT_TIMESTAMP N Y textdate 30 Y Y N Date/time this was performed
MA_hybridization 6 prehyb_chamber PreHyb Chamber varchar 25 0 Y N N text 10 Y Y N
MA_hybridization 7 hyb_chamber Hyb Chamber varchar 25 0 Y N N text 10 Y Y N
MA_hybridization 8 wash_chamber Wash Chamber varchar 25 0 Y N N text 10 Y Y N
MA_hybridization 9 deviations Deviations from Protocol varchar 1000 0 Y N N textarea 4 Y Y N Text describing any deviations from the protocol or other comments
MA_hybridization 10 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_hybridization 11 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_hybridization 12 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_hybridization 13 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_hybridization 14 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_hybridization 15 record_status Record Status char 1 0 N N N N N
MA_array_scan 1 array_scan_id Array Scan ID int 8 0 N Y N N pkDEFAULT
MA_array_scan 2 array_id Array Name int 8 0 N N MA_array array_id Y scrolloptionlist 4 setDefaultImagesLocation() Y Y Y Array Name which was scanned "SELECT A.array_id,array_name||CASE WHEN S.array_id IS NOT NULL THEN ' - *DONE*' ELSE '' END, S.array_id FROM $TBMA_ARRAY A LEFT JOIN $TBMA_ARRAY_SCAN S ON ( A.array_id=S.array_id ) WHERE A.record_status != 'D' ORDER BY A.array_name"
MA_array_scan 3 protocol_id Protocol int 8 0 N N protocol protocol_id Y optionlist Y Y N Protocol used for scanning "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='array_scanning' ORDER BY P.name"
MA_array_scan 4 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 4 Y Y N List any deviations from the selected protocol
MA_array_scan 5 resolution Resolution float 8 0 Y N Y text 10 Y Y N Scan resolution in microns
MA_array_scan 6 stage_location Orig Data Location varchar 255 0 Y N Y text 60 refreshDocument() Y Y Y Location of the source data directory (containing the Images/ subdirectory)
MA_array_scan 7 uri Data URI varchar 255 0 Y N N text 60 N N N Internal database URI for data directory SELF
MA_array_scan 8 data_flag Data Flag varchar 10 0 N N Y optionlist Y Y N "OK, or set to BAD if this scan should not be processed" "SELECT option_key,option_value FROM $TBMA_MISC_OPTION WHERE option_type='data_flag' ORDER BY sort_order,option_value"
MA_array_scan 9 date_scanned Date Scanned datetime 8 0 N CURRENT_TIMESTAMP N N textdate 30 Y Y N Date and time the slide was scanned (optional; will be replaced with file timestamps eventually)
MA_array_scan 10 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Optional comment about this particular microarray scan
MA_array_scan 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_scan 12 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_array_scan 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_scan 14 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_array_scan 15 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_array_scan 16 record_status Record Status char 1 0 N N N N N
MA_array_quantitation 1 array_quantitation_id Array Quantitation ID int 8 0 N Y N N pkDEFAULT
MA_array_quantitation 2 array_scan_id Array Name int 8 0 N N MA_array_scan array_scan_id Y scrolloptionlist 4 setDefaultQALocation() Y Y Y Array Name which was quantitated MANUAL
MA_array_quantitation 3 protocol_id Protocol int 8 0 N N protocol protocol_id Y optionlist Y Y N Protocol used for spot finding "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='image_analysis' ORDER BY P.name"
MA_array_quantitation 4 stage_location Orig Data Location varchar 255 0 Y N Y text 60 refreshDocument() Y Y Y Location of the output data file
MA_array_quantitation 5 uri Data URI varchar 255 0 Y N N text 60 N N N Internal database URI for data directory
MA_array_quantitation 6 data_flag Data Flag varchar 10 0 N N Y optionlist Y Y N "OK, or set to BAD if this quantitation should not be processed" "SELECT option_key,option_value FROM $TBMA_MISC_OPTION WHERE option_type='data_flag' ORDER BY sort_order,option_value"
MA_array_quantitation 7 date_quantitated Date Quantitated datetime 8 0 N CURRENT_TIMESTAMP N N textdate 30 Y Y N Date and time the slide was quantitated (optional; will be replaced with file timestamps eventually)
MA_array_quantitation 8 comment Comment varchar 255 0 Y N N textarea 4 Y Y N Optional comment about this particular quantitation
MA_array_quantitation 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_quantitation 10 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_array_quantitation 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_array_quantitation 12 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_array_quantitation 13 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_array_quantitation 14 record_status Record Status char 1 0 N N N N N
MA_biosequence_set 1 biosequence_set_id BioSequence Set ID int 4 0 N Y N N pkDEFAULT
MA_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"
MA_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"
MA_biosequence_set 4 set_name Set Name varchar 100 0 N N Y text 50 Y Y N Name of this BioSequence database
MA_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
MA_biosequence_set 6 set_description Set Description varchar 255 0 N N Y text 50 Y Y N Longer description of this BioSequence database
MA_biosequence_set 7 set_version Set Version varchar 50 0 N N Y text 40 Y Y N Version of this BioSequence database
MA_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"
MA_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
MA_biosequence_set 10 set_path Set Path varchar 255 0 N N Y text 50 Y Y N File path of this BioSequence database
MA_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
MA_biosequence_set 12 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF
MA_biosequence_set 13 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments
MA_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.
MA_biosequence_set 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_biosequence_set 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N
MA_biosequence_set 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_biosequence_set 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N
MA_biosequence_set 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_biosequence_set 20 record_status Record Status char 1 0 N N N N N
MA_channel 1 channel_id Channel ID int 8 0 N Y N N pkDEFAULT
MA_channel 2 channel_name Channel Name varchar 50 0 N N Y text 50 Y Y Y Channel Name
MA_channel 3 channel_desc Channel Description varchar 255 0 Y N N textarea 4 Y Y N Channel Descrption
MA_channel 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_channel 5 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_channel 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_channel 7 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_channel 8 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_channel 9 record_status Record Status char 1 0 N N N N N
MA_server 1 server_id Server ID int 8 0 N Y N N pkDEFAULT
MA_server 2 server_name Server Name varchar 50 0 N N Y text 50 Y Y Y Server Name
MA_server 3 server_desc Server Description varchar 255 0 Y N N textarea 4 Y Y N Server Description
MA_server 4 server_ip Server IP varchar 15 0 Y N N text 50 Y Y N Server IP
MA_server 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_server 6 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_server 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_server 8 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_server 9 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_server 10 record_status Record Status char 1 0 N N N N N
MA_file_path 1 file_path_id File Path ID int 8 0 N Y N N pkDEFAULT
MA_file_path 2 file_path_name File Path Name varchar 50 0 N N Y text 50 Y Y Y File Path Name
MA_file_path 3 file_path_desc File Path Description varchar 255 0 Y N N text 50 Y Y N File Path Description
MA_file_path 4 file_path File Path varchar 2000 0 N N Y text 50 Y Y N File Path
MA_file_path 5 server_id Server ID int 8 0 N N server server_id Y optionlist Y Y N Server ID "SELECT server_id,server_name FROM $TBMA_SERVER WHERE record_status != 'D'"
MA_file_path 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_file_path 7 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_file_path 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_file_path 9 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_file_path 10 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_file_path 11 record_status Record Status char 1 0 N N N N N
MA_file_location 1 file_location_id File Location int 8 0 N Y N N Y File Location ID pkDEFAULT
MA_file_location 2 file_name File Name varchar 2000 0 N N Y text 50 Y Y N Name of File
MA_file_location 3 file_type_id File Type ID int 8 0 N N MA_file_type file_type_id Y optionlist Y Y Y File Type ID "SELECT file_type_id, file_type_name FROM $TBMA_FILE_TYPE WHERE record_status != 'D'"
MA_file_location 4 file_path_id File Path ID int 8 0 N N MA_file_path file_path_id Y optionlist Y Y Y File Path ID "SELECT file_path_id, file_path_name FROM $TBMA_FILE_PATH WHERE record_status != 'D'"
MA_file_location 5 file_size File Size int 8 0 Y N N N N File Size
MA_file_location 6 digital_signature Digital Signature varchar 2000 0 Y N N N N Digital Signature
MA_file_location 7 file_zipped_flag File Zipped Flag bit 1 0 N N N N N
MA_file_location 8 file_name_zipped File Name Zipped varchar 2000 0 Y N N N N Zipped File Name
MA_file_location 9 file_size_zipped File Size Zipped int 8 0 Y N N N N Zipped File Size
MA_file_location 10 digital_signature_zipped Digital Signature Zipped varchar 2000 0 Y N N N N
MA_file_location 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_file_location 12 created_by_id Record Created By int 8 0 N N contact contact_id N N Y
MA_file_location 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_file_location 14 modified_by_id Record Modified By int 8 0 N N contact contact_id N N Y
MA_file_location 15 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N Y
MA_file_location 16 record_status Record Status char 1 0 Y N N N N N
MA_file_type 1 file_type_id File Type ID int 8 0 N Y N N File Type ID pkDEFAULT
MA_file_type 2 file_type_name File Type Name varchar 50 0 N N Y text 50 Y Y Y File Type Name
MA_file_type 3 file_type_desc File Type Description varchar 255 0 Y N N textarea 4 Y Y N File Type Description
MA_file_type 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_file_type 5 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_file_type 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_file_type 7 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_file_type 8 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_file_type 9 record_status Record Status char 1 0 Y N N N N
MA_quantitation_type 1 quantitation_type_id Quantitation Type ID int 8 0 N Y N N Quantitation Type ID pkDEFAULT
MA_quantitation_type 2 quantitation_type_name Quantitation Type Name varchar 50 0 N N Y text 50 Y Y Y Quantitation Type Name
MA_quantitation_type 3 quantitation_type_desc Quantitation Type Description varchar 255 0 Y N N textarea 4 Y Y N Quantitation Type Description
MA_quantitation_type 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_quantitation_type 5 created_by_id Record Created By int 8 0 N N contact contact_id N N
MA_quantitation_type 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_quantitation_type 7 modified_by_id Record Modified By int 8 0 N N contact contact_id N N
MA_quantitation_type 8 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N
MA_quantitation_type 9 record_status Record Status char 1 0 Y N N N N
MA_GetExpression 1 project_id Projects Y multioptionlist 4 refreshDocument() Y Y N Constrain conditions to one or more projects. At least one project must be selected. "SELECT DISTINCT P.project_id,UL.username||' - '||P.name FROM $TB_PROJECT P INNER JOIN $TBMA_COMPARISON_CONDITION C ON ( P.project_id = C.project_id ) 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 UL.username||' - '||P.name,P.project_id"
MA_GetExpression 2 condition_id Comparison Conditions N multioptionlist 10 Y Y N "Constrain Interactions to selected Projects. MultipleProjects may be selected. If no Projects are selected, ALLProjects are searched." MANUAL
MA_GetExpression 3 gene_name_constraint Gene Name Constraint N text 40 Y Y N Constraint for the Gene Name as provided in the raw pipeline output. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 4 second_name_constraint Second Name Constraint N text 40 Y Y N Constraint for the Second Name as provided in the raw pipeline output. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 5 biosequence_name_constraint Biosequence 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.
MA_GetExpression 6 common_name_constraint Common Name Constraint N text 40 Y Y N Constraint for the Common Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 7 canonical_name_constraint Canonical Name Constraint N text 40 Y Y N Constraint for the Canonical Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 8 description_constraint Biosequence 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.
MA_GetExpression 9 reporter_name_constraint Reporter Name Constraint N text 40 Y Y N Constraint for the Reporter Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 10 log10_ratio_constraint log10 Ratio Constraint N text 20 Y Y N "Constraint for the log 10 ratio of expression. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetExpression 11 p_value_constraint P Value Constraint N text 20 Y Y N "Constraint for the P value of expression. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetExpression 12 lambda_constraint Lambda Constraint N text 20 Y Y N "Constraint for the lamba value of expression. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetExpression 13 mean_intensity_constraint Mean Level Constraint N text 20 Y Y N "Constraint for the Mean Level . Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetExpression 14 false_discovery_rate_constraint False Discovery Constraint N text 20 Y Y N "Constraint for the false discovery rate . Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetExpression 15 mu_x_or_mu_y_constraint Either channel intensity Constraint N text 20 Y Y N "Constraint for either channel intensity (constraint applies to mu_x OR mu_y) . Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetExpression 16 display_columns Data Columns to Display N multioptionlist 4 Y Y N Desired data columns to display (or pivot) for the expression measurements "SELECT option_key,option_value FROM $TBMA_QUERY_OPTION WHERE option_type = 'GE_data_columns' ORDER BY sort_order,option_value"
MA_GetExpression 17 molecular_function_constraint Molecular Function Constraint N text 40 Y N N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 18 biological_process_constraint Biological Process Constraint N text 40 Y N N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 19 cellular_component_constraint Cellular Component Constraint N text 40 Y N N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetExpression 20 sort_order Sort Order N optionlist Y N N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBMA_QUERY_OPTION WHERE option_type = 'GE_sort_options' ORDER BY sort_order,option_value"
MA_GetExpression 21 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBMA_QUERY_OPTION WHERE option_type = 'GE_display_options' ORDER BY sort_order,option_value"
MA_GetExpression 22 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 10000 rows."
MA_affy_array_sample 1 affy_array_sample_id Affy Array Sample ID int 4 0 N Y Y N N Y Affy Array Sample ID pkDEFAULT
MA_affy_array_sample 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y N FK to project.project_id "SELECT project_id, UL.username || ' - ' || proj.name || ' ( ' || RTRIM(CAST(proj.project_id AS CHAR)) || ' )' AS name FROM $TB_PROJECT proj JOIN $TB_USER_LOGIN UL ON (proj.PI_contact_id = UL.contact_id) WHERE proj.project_id IN ( $accessible_project_ids ) AND proj.project_tag IS NOT NULL AND proj.record_status != 'D' ORDER BY UL.username"
MA_affy_array_sample 3 sample_tag Sample Tag varchar 50 0 N N Y text 50 Y Y N Sample Name. Keep it short. Do not use any strange characters like /\*&$() (e.g. NP Epi 03-123)
MA_affy_array_sample 4 full_sample_name Full Sample Name varchar 255 0 Y N Y textarea 3 Y Y N "Full Sample Name. A longer, less cryptic name should be placed here. It should be long enough so that someone else can understand quickly the general idea of the sample. (e.g. Epithelial cells FACS sorted from ""normal"" prostate tissue from specimen 03-123)"
MA_affy_array_sample 5 sample_group_name Sample Group Name varchar 50 0 Y N Y text 50 Y Y N Sample Group Name. Name used to group together biological replicates
MA_affy_array_sample 6 sample_provider_organization_id Sample Provider int 4 0 Y N organization organization_id N optionlist Y Y N "Provider of this biomaterial (academic department, research lab, vendor, etc.)" "SELECT O.organization_id,O.organization FROM $TB_ORGANIZATION O INNER JOIN $TB_ORGANIZATION_TYPE OT ON (O.organization_type_id=OT.organization_type_id) WHERE O.record_status != 'D' ORDER BY organization"
MA_affy_array_sample 7 organism_id Organism int 4 0 Y N organism organism_id N optionlist Y Y N Organism from which the biomaterial was derived "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"
MA_affy_array_sample 8 strain_or_line Strain or Line varchar 255 0 Y N N text 50 Y Y N Strain or line of the individual
MA_affy_array_sample 9 individual Individual varchar 255 0 Y N N text 50 Y Y N Identifier or name of the individual organism from which the biomaterial was derived
MA_affy_array_sample 10 sex_ontology_term_id Sex int 4 0 Y N N optionlist Y Y N Sex of the individual MANUAL
MA_affy_array_sample 11 age Age varchar 255 0 Y N N text 50 Y Y N "Age of the individual at the time of harvest of the biomaterial. Free form text; include units, developmental stage, and reference point as appropriate (e.g., days since planting, years after birth, minutes after death)"
MA_affy_array_sample 12 organism_part Organism Part varchar 255 0 Y N N text 50 Y Y N "Part of the organism's anatomy from the biomaterial was derived, excludes cells. (e.g., tissue, organ, system, or body location)"
MA_affy_array_sample 13 cell_line Cell Line varchar 255 0 Y N N text 50 Y Y N Identifier for the cell line if one was used as a biomaterial
MA_affy_array_sample 14 cell_type Cell Type varchar 255 0 Y N N text 50 Y Y N "Type of cell used as the biomaterial (e.g., epithelial, glial, etc.)"
MA_affy_array_sample 15 disease_state Disease State varchar 255 0 Y N N text 50 Y Y N "Name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is ""normal"" if no disease state has been diagnosed."
MA_affy_array_sample 16 rna_template_mass Starting Amount of RNA (ng) float 8 0 Y N N text 50 Y Y N Amount of RNA used as input into the labeling reaction. Measured in nanograms
MA_affy_array_sample 17 affy_sample_protocol_ids Affy Array Sample Protocols varchar 255 0 Y N MA_affy_array_sample_protocol affy_array_sample_protocol_id N multilink 4 Y Y N Select all protocols that apply to this biomaterial. Describe sequence of protocols in the Treatment Description below "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 P.record_status != 'D' ORDER BY P.name"
MA_affy_array_sample 18 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 4 Y Y N Describe any deviations from the selected protocols
MA_affy_array_sample 19 sample_description Sample Description text 16 0 Y N N textarea 4 Y Y N Describe the biomaterial briefly
MA_affy_array_sample 20 sample_preparation_date Sample Preparation Date datetime 8 0 N N N text 30 Y Y Y Date/time the biomaterial was prepared with the described protocols
MA_affy_array_sample 21 treatment_description Treatment Description text 16 0 Y N N textarea 4 Y Y N "Describe the treatment of the biomaterials, including mention of the selected protocols"
MA_affy_array_sample 22 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional notes
MA_affy_array_sample 23 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N Y N
MA_affy_array_sample 24 created_by_id Record Created By int 4 0 N N contact contact_id N N Y
MA_affy_array_sample 25 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_array_sample 26 modified_by_id Record Modified By int 4 0 N N contact contact_id N N Y
MA_affy_array_sample 27 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y
MA_affy_array_sample 28 record_status Record Status char 1 0 N N N N N N
MA_affy_array 1 affy_array_id Affy Array ID int 4 0 N Y Y N N Y Affy Array ID pkDEFAULT
MA_affy_array 2 file_root Root File Name varchar 100 0 N N Y fixed 50 Y Y N Root Name of the affy data file. No file extensions are needed
MA_affy_array 3 file_path_id File Path int 4 0 N N MA_file_path file_path_id Y optionlist 2 Y Y Y Select the Root file path for the group of files generated from this array. FK to MA_file_path.file_path_id "SELECT file_path_id , file_path FROM $TBMA_FILE_PATH WHERE record_status != 'D'"
MA_affy_array 4 array_type_id Array Type int 4 0 N N MA_slide_type slide_type_id Y optionlist Y Y Y Pick an Affy Array type from the drop down. FK to MA_slide_type.slide_type_id "SELECT slide_type_id , name FROM $TBMA_SLIDE_TYPE WHERE record_status != 'D'"
MA_affy_array 5 processed_date Processed Date datetime 8 0 N N Y text 50 Y Y N Date the array was scanned
MA_affy_array 6 affy_array_sample_id Affy Array Sample int 4 0 N N MA_affy_array_sample affy_array_sample_id Y optionlist 15 Y Y Y Pick and Affy Array sample tag from the drop down. FK to MA_affy_array_sample.affy_array_sample_id "SELECT affy_array_sample_id, sample_tag FROM $TBMA_AFFY_ARRAY_SAMPLE WHERE project_id = $project_id AND record_status != 'D'"
MA_affy_array 7 user_id User int 4 0 Y N user_login user_login_id N optionlist Y Y Y Select the User who requested to have this Array processed. FK to user_login.user_login_id "SELECT user_login_id, username FROM $TB_USER_LOGIN WHERE record_status != 'D'"
MA_affy_array 8 affy_array_protocol_ids Affy Array Protocols varchar 255 0 Y N MA_affy_array_protocol affy_array_protocol_id N multilink 4 Y Y N Select all protocols that apply to this array. Describe sequence of protocols in the Treatment Description below "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 P.record_status != 'D' ORDER BY P.name"
MA_affy_array 9 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 4 Y Y N Describe any deviations from the selected protocols
MA_affy_array 10 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional notes
MA_affy_array 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N Y N
MA_affy_array 12 created_by_id Record Created By int 4 0 N N contact contact_id N N Y
MA_affy_array 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_array 14 modified_by_id Record Modified By int 4 0 N N contact contact_id N N Y
MA_affy_array 15 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y
MA_affy_array 16 record_status Record Status char 1 0 N N N N N N
MA_affy_array_sample_protocol 1 affy_array_sample_protocol_id Affy Array Sample Protocol int 4 0 N Y Y N N N pkDEFAULT
MA_affy_array_sample_protocol 2 affy_array_sample_id Affy Array Sample int 4 0 N N MA_affy_array_sample affy_array_sample_id Y Y N Y FK to MA_affy_array_sample.affy_array_sample_id
MA_affy_array_sample_protocol 3 protocol_id Protocol ID int 4 0 N N protocol protocol_id Y N N Y Protocol ID
MA_affy_array_sample_protocol 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_affy_array_sample_protocol 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N
MA_affy_array_sample_protocol 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_affy_array_sample_protocol 7 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N
MA_affy_array_sample_protocol 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_affy_array_sample_protocol 9 record_status Record Status char 1 0 N N N N N
MA_affy_array_protocol 1 affy_array_protocol_id Affy Array Protocol int 4 0 N Y N N N pkDEFAULT
MA_affy_array_protocol 2 affy_array_id Affy Array ID int 4 0 N N MA_affy_array affy_array_id Y Y N Y FK to MA_affy_array.affy_array_id
MA_affy_array_protocol 3 protocol_id Protocol ID int 4 0 N N protocol protocol_id Y N N Y Protocol ID
MA_affy_array_protocol 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N Y
MA_affy_array_protocol 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N
MA_affy_array_protocol 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N
MA_affy_array_protocol 7 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N
MA_affy_array_protocol 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_affy_array_protocol 9 record_status Record Status char 1 0 N N N N N
MA_affy_gene_intensity 1 affy_gene_intensity_id Affy Gene Intensity ID int 4 0 N Y N N Y
MA_affy_gene_intensity 2 probe_set_id Probe Set ID varchar 50 0 N N Y N N Y affymetix probe set name example '1007_s_at'
MA_affy_gene_intensity 3 affy_array_id Affy Array ID int 4 0 N N MA_affy_array affy_array_id Y N N Y
MA_affy_gene_intensity 4 signal Signal float 8 0 N N Y N N
MA_affy_gene_intensity 5 detection_call Detection Call char 1 0 N N Y N N
MA_affy_gene_intensity 6 detection_p_value Detection P Value float 8 0 N N Y N N
MA_affy_gene_intensity 7 protocol_id Protocol ID int 4 0 N N protocol protocol_id Y N N
MA_affy_annotation 1 affy_annotation_id Affy Annotation ID int 4 0 N Y N N N
MA_affy_annotation 2 affy_annotation_set_id Annotation Set ID int 4 0 N N MA_affy_annotation_set affy_annotation_set_id Y Y N Y FK to MA_affy_annotation_set
MA_affy_annotation 3 probe_set_id Probe Set ID varchar 50 0 N N Y Y Y N affymetix probe set name example '1007_s_at'
MA_affy_annotation 4 sequence_type Sequence Type varchar 50 0 Y N Y Y N "Indicates whether the sequence is an Exemplar, Consensus or Control sequence. An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database."
MA_affy_annotation 5 sequence_source Sequence Source varchar 50 0 Y N Y Y N The database from which the sequence used to design this probe set was taken.
MA_affy_annotation 6 transcript_id Transcript ID varchar 50 0 Y N Y Y N "Cluster identification number with a sub-cluster identifier appended. Currently provided only for HG-U133, HG-Focus, and newer arrays."
MA_affy_annotation 7 target_description_feature GB Feature varchar 255 0 Y N Y Y N GenBank description associated with the representative public identifier. Blank for some probe sets.
MA_affy_annotation 8 target_description GB Description varchar 255 0 Y N Y Y N GenBank description associated with the representative public identifier. Blank for some probe sets.
MA_affy_annotation 9 target_description_note GB Note varchar 255 0 Y N Y Y N "Parsed from the Target Description column contains information about what part of the gene the probe set targets, used manily to describe the affy controls on the chip"
MA_affy_annotation 10 representative_public_id Representative Public ID varchar 50 0 Y N Y Y N The accession number of a representative sequence.
MA_affy_annotation 11 archival_unigene_cluster Archival UniGene Cluster varchar 50 0 Y N Y Y N
MA_affy_annotation 12 gene_title Gene Title varchar 255 0 Y N Y Y N
MA_affy_annotation 13 gene_symbol Gene Symbol varchar 50 0 Y N Y Y N
MA_affy_annotation 14 chromosomal_location Chromosomal Location varchar 50 0 Y N Y Y N Chromosomal Band
MA_affy_annotation 15 pathway Patway varchar 255 0 Y N Y Y N References to Gene MicroArray Pathway Profiler and KEGG: Kyoto Encyclopedia of Genes and Genomes.
MA_affy_annotation 16 qtl QTL varchar 100 0 Y N Y Y N Quantitative Trait Loci (QTL) are genetic linkage data that provide disease associations for various loci.
MA_affy_annotation 17 annotation_description Annotation Description varchar 255 0 Y N Y Y N Affymetrix annotation information. Description of the method used to annotate the probe set.
MA_affy_annotation 18 transcript_assignment Transcript Assignment varchar 255 1 Y N Y Y N Affymetrix annotation information. Contains the mRNA to probe set assignments.
MA_affy_annotation 19 annotation_transcript_cluster Annotation Transcript Cluster varchar 255 2 Y N Y Y N Affymetrix annotation information. Contains the IDs of the transcripts used in the transcript to gene annotation mapping.
MA_affy_annotation 20 annotation_notes Annotation Notes varchar 255 3 Y N Y Y N Affymetrix annotation information. Contains assignments cross hyb and negative strand alignments.
MA_affy_db_links 1 affy_db_links_id Affy DB Links ID int 4 0 N Y N N Y
MA_affy_db_links 2 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id Y N N N FK to MA_affy_annotaion
MA_affy_db_links 3 dbxref_id DBXref ID int 4 0 N N Y N N N FK to proteomic dbxref table
MA_affy_db_links 4 db_id DB ID varchar 50 0 N N Y Y N N Accession number to foregin database
MA_affy_annotation_set 1 affy_annotation_set_id Annotation Set ID int 4 0 N Y N N Y
MA_affy_annotation_set 2 annotation_date Affy Annotation Date varchar 50 1 N N Y text 50 Y Y N Date of the Affy annot.csv file is made by Affymetrix (DATE LEFT IN AFFY FORMAT)
MA_affy_annotation_set 3 slide_type_id Array Type int 4 2 N N Y optionlist 2 N Y Y Slide Type ID
MA_affy_annotation_set 4 genome_version Genome Version varchar 50 3 N N Y text 50 Y Y N Version of the Genome used by Affymetrix to generate data for Alignments column
MA_affy_annotation_set 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_annotation_set 6 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N Y
MA_affy_annotation_set 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_annotation_set 8 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N Y
MA_affy_annotation_set 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y
MA_affy_annotation_set 10 record_status Record Status char 1 0 N N N N N N
MA_comparison_condition 1 condition_id Condition ID int 4 10 N Y N N Y pkDEFAULT
MA_comparison_condition 2 project_id Project ID int 4 10 N N project project_id Y optionlist Y Y Y "SELECT project_id, username||' - '||name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN US ON ( P.PI_contact_id=US.contact_id ) WHERE project_id IN ( $accessible_project_ids ) AND P.record_status != 'D' ORDER BY name"
MA_comparison_condition 3 condition_name Condition name varchar 255 255 N N Y fixed 50 Y Y Y Name for the condition
MA_comparison_condition 4 condition_file_name Condition file name varchar 255 255 Y N N fixed 50 Y Y N Original filename or identifier for a processed condition. May not be changed
MA_comparison_condition 5 sort_order Sort Order int 4 10 N 100 N N text 10 Y Y N
MA_comparison_condition 6 processed_date Precessed Date datetime 8 23 Y N N fixed Y Y N
MA_comparison_condition 7 organism_id Organism int 4 0 Y N organism organism_id Y optionlist Y Y N Organism which the condition should be associated with. Leave blank if not applicable "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"
MA_comparison_condition 8 analysis_type Analysis Type varchar 255 255 Y N N fixed Y Y N
MA_comparison_condition 9 analysis_id Analysis ID int 4 10 Y N N fixed Y Y N
MA_comparison_condition 10 comment Comment text 16 16 Y N N textarea 5 Y Y N
MA_comparison_condition 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_comparison_condition 12 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N Y
MA_comparison_condition 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_comparison_condition 14 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N Y
MA_comparison_condition 15 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y
MA_comparison_condition 16 record_status Record Status char 1 0 N N N N N N
MA_gene_expression 1 gene_expression_id Gene Expression Id int 4 10 N Y N N Y
MA_gene_expression 2 condition_id Condition name int 4 10 N N MA_comparison_condition condition_id Y Y Y
MA_gene_expression 3 reporter_name Reporter Name varchar 255 255 Y N Y Y N
MA_gene_expression 4 common_name Common Name varchar 255 255 Y N Y Y N
MA_gene_expression 5 canonical_name Canonical Name varchar 255 255 Y N Y Y N
MA_gene_expression 6 full_name Full Name varchar 1024 1024 Y N Y Y N
MA_gene_expression 7 gene_name Gene Name varchar 255 255 Y N Y Y N
MA_gene_expression 8 external_identifier External Identifier varchar 255 255 Y N Y Y N
MA_gene_expression 9 second_name Second Name varchar 255 255 Y N Y Y N
MA_gene_expression 10 biosequence_id BioSequence ID int 4 10 Y N Y Y N
MA_gene_expression 11 log10_ratio log10 Ratio real 4 7 Y N Y Y N
MA_gene_expression 12 log10_uncertainty log10 Ratio real 4 7 Y N Y Y N
MA_gene_expression 13 log10_std_deviation log10 Std Deviation real 4 7 Y N Y Y N
MA_gene_expression 14 lambda Lambda real 4 7 Y N Y Y N
MA_gene_expression 15 mu_x Mu X real 4 7 Y N Y Y N
MA_gene_expression 16 mu_y mu Y real 4 7 Y N Y Y N
MA_gene_expression 17 p_value P Value real 4 7 Y N Y Y N
MA_gene_expression 18 mean_intensity Mean Intensity real 4 7 Y N Y Y N
MA_gene_expression 19 mean_intensity_uncertainty Mean Intensity Uncertainty real 4 7 Y N Y Y N
MA_gene_expression 20 quality_flag Quality Flag varchar 25 25 Y N Y Y N
MA_gene_expression 21 false_discovery_rate False Discovery Rate real 4 7 Y N Y Y N
MA_overlapping_transcript 1 overlapping_transcript_id Overlapping Transcript ID int 4 0 N Y Y Data parsed from Overlapping Transcripts Column
MA_overlapping_transcript 2 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id Y
MA_overlapping_transcript 3 accession_number Accession Number varchar 50 0 Y N Details of overlapping transcripts found in a chromosomal region that aligns with a target sequence.
MA_overlapping_transcript 4 title Title varchar 255 0 Y N Details of overlapping transcripts found in a chromosomal region that aligns with a target sequence.
MA_overlapping_transcript 5 overlapping_gene_start Gene Start bp int 4 0 Y N Details of overlapping transcripts found in a chromosomal region that aligns with a target sequence.
MA_overlapping_transcript 6 overlapping_gene_end Gene End bp int 4 0 Y N Details of overlapping transcripts found in a chromosomal region that aligns with a target sequence.
MA_overlapping_transcript 7 overlapping_choromosome Chromosomal Location varchar 25 0 Y N Details of overlapping transcripts found in a chromosomal region that aligns with a target sequence.
MA_overlapping_transcript 8 gene_orientation Gene Orientation char 1 0 Y N Details of overlapping transcripts found in a chromosomal region that aligns with a target sequence.
MA_gene_ontology 1 gene_ontology_id Gene Ontology ID int 4 0 N Y Y
MA_gene_ontology 2 gene_ontology_type_id Ontology Type ID int 4 0 N N MA_gene_ontology_type gene_ontology_type_id Y
MA_gene_ontology 3 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id Y
MA_gene_ontology 4 affy_db_links_id Affy DB Links ID int 4 0 N N MA_affy_db_links affy_db_links_id Y Will hold the Go Ontology Accession number
MA_gene_ontology 5 affy_gene_ontology_id Affy gene ontology id int 4 0 N N Y "Affy Gene ontology ID, which is not the full ontology ID. Example 1234 should be GO:001234"
MA_gene_ontology 6 gene_ontology_description Ontology Description varchar 255 0 Y N The description corresponds directly to the GO ID.
MA_gene_ontology 7 gene_ontology_evidence Ontology Evidence varchar 255 0 Y N "The evidence can be ""direct"", or ""extended"". Direct evidence: shows the type of evidence provided by the GO Consortium for their curation of a relationship between the LocusLink accession and the GO Ontology term. Extended evidence: indicates that the Ontology term was curated by Affymetrix Inc. based on similarity with genes that are annotated by the GO Consortium."
MA_gene_ontology_type 1 gene_ontology_type_id Gene Ontology Type ID int 4 0 N Y Y
MA_gene_ontology_type 2 gene_ontology_name_type Gene Ontology Name Type varchar 100 0 N N Y "One of three types of annotation, Biological Process (GO), Cellular Component (GO), Molecular Function (GO) "
MA_protein_families 1 protein_families_id Protein Families ID int 4 0 N Y Y
MA_protein_families 2 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id Y
MA_protein_families 3 affy_db_links_id Affy DB Links ID int 4 0 N N MA_affy_db_links affy_db_links_id Y "References to entries in the various databases, indicated by namespace prefixes. Examples GPCR, EC, P450, HANKS"
MA_protein_families 4 description Protein Families Description varchar 255 0 Y N
MA_protein_families 5 e_value E value float 8 0 Y N
MA_trans_membrane 1 trans_membrane_id Transmembrane ID int 4 0 N Y Y
MA_trans_membrane 2 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id
MA_trans_membrane 3 number_of_domains Number of Transmembrane Domains int 4 0 Y N number of transmembrane domains
MA_trans_membrane 4 nin_prob Probability that the N-terminus is interior float 8 0 Y N the probability that the N-terminus is interior
MA_trans_membrane 5 type Transmembrane Type varchar 50 0 Y N "SIGNAL"", ""ANCHOR"" or empty """""
MA_trans_membrane 6 protein_accession_numb Protein Accession Number varchar 25 0 Y N Accession number for the protein used in the TM prediction program. New fields as of 10.25.04
MA_trans_membrane_domain 1 trans_membrane_domain_id Transmembrane Type ID int 4 0 N Y Y
MA_trans_membrane_domain 2 trans_membrane_id Transmembrane ID int 4 0 N N MA_trans_membrane trans_membrane_id Y
MA_trans_membrane_domain 3 tm_protein_start TM Protein Start int 4 0 Y N Start of the transmembrane prediction
MA_trans_membrane_domain 4 tm_protein_end TM Protein End int 4 0 Y N End of the transmembrane prediciton
MA_trans_membrane_domain 5 tm_e_value E value float 8 0 Y N
MA_interpro 1 interpro_id Interpro_id int 4 0 N Y Y
MA_interpro 2 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id Y
MA_interpro 3 affy_db_links_id Affy DB Links ID int 4 0 N N MA_affy_db_links affy_db_links_id Y InterPro accession number and description.
MA_interpro 4 interpro_description Interpro Description varchar 255 0 Y N InterPro accession number and description.
MA_protein_domain 1 protein_domain_id Protein Domain ID int 4 0 N Y Y
MA_protein_domain 2 affy_annotation_id Affy Annotation ID int 4 0 N N MA_affy_annotation affy_annotation_id Y
MA_protein_domain 3 affy_db_links_id Affy DB Links ID int 4 0 N N MA_affy_db_links affy_db_links_id Y
MA_protein_domain 4 protein_domain_description Protein Domain Description varchar 255 0 N N Pfam or SCOP annotations
MA_protein_domain 5 protein_domain_e_value Protein Domain E-value float 8 0 Y N An E-value reveals how well the RefSeq peptide sequence corresponding to our probe set matches to the sequence in question. Smaller numbers are better..
MA_alignment 1 alignment_id Alignment ID int 4 N Y
MA_alignment 2 affy_annotation_id Affy Annotation ID int 4 N N MA_affy_annotation affy_annotation_id Y
MA_alignment 3 gene_start Gene Start bp int 4 0 N N Y Y Y N Position of the alignment of the target sequence on the genome. Parsed from Alignments Column
MA_alignment 4 gene_stop Gene Stop bp int 4 0 Y N Y Y N Position of the alignment of the target sequence on the genome. Parsed from Alignments Column
MA_alignment 5 percent_identity Gene Percent Identity float 8 0 Y N Y Y N percentage identity of target sequence on the genome. Parsed from Alignments Column
MA_alignment 6 gene_orientation Gene Orientation char 1 0 Y N Y Y N Strand of the genomic alignment. Parsed from Alignments Column
MA_alignment 7 match_chromosome Match Chromosomal varchar 25 0 Y N Y Y N Chromosome gene aligns to
MA_GetAffy_GeneIntensity 1 project_id Projects Y multioptionlist 4 refreshDocument() Y Y N Constrain affy arrays to one or more projects. At least one project must be selected. MANUAL
MA_GetAffy_GeneIntensity 2 affy_array_id Affy Arrays Constraint N multioptionlist 10 Y Y N "Constraint Affy Arrays to selected Projects. MultipleProjects may be selected. If no Projects are selected, ALLProjects are searched." MANUAL
MA_GetAffy_GeneIntensity 3 annotation_set_constraint Annotation Set Name N multioptionlist 5 Y 1 N Annotation Set Name. Choose a previous annotation set. Default to Newest Data set MANUAL
MA_GetAffy_GeneIntensity 4 protocol_id_constraint Array Analysis Protocol N optionlist 10 refreshDocument() Y 2 N Protocol ID Used to convert the Affy CEL file to a R_CHP file "SELECT distinct (prot.protocol_id), prot.name FROM $TB_PROTOCOL prot WHERE prot.name like 'R %'"
MA_GetAffy_GeneIntensity 5 probe_set_id_constraint Affy Probe Set Id N text 20 Y Y N Affy Probe Set ID Example '239122_at'
'%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetAffy_GeneIntensity 6 gene_symbol_constraint Gene Symbol Constraint N text 20 Y Y N Constraint for the Gene Symbol. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetAffy_GeneIntensity 7 gene_title_constraint Gene Title Constraint N text 40 Y Y N Constraint for the Gene Title: '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetAffy_GeneIntensity 8 detection_call_constraint Detection Call N text 20 Y Y N R_CHP Detection Call 'P' or 'A' or 'M'
'%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetAffy_GeneIntensity 9 detection_p_value_constraint Detection P Value N text 10 Y Y N "R_CHP Detection Call P-value
Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetAffy_GeneIntensity 10 signal_constraint Signal N text 20 Y Y N "R_CHP Signal Value
Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetAffy_GeneIntensity 11 go_description_constraint GO Constraint N text 20 Y 1 N "Go Description constriant. Search All GO types (Biological Process, Molecular Function, Cellular Component) for a term of interest. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported."
MA_GetAffy_GeneIntensity 12 trans_membrane_constraint Trans Membrane Constraint N text 10 Y 2 N "Constraint on the number of transmembrane domains
Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""
MA_GetAffy_GeneIntensity 13 protein_families_constraint Protein Families Constraint N text 20 Y 2 N Constriant on the protein family. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetAffy_GeneIntensity 14 protein_domain_constraint Protein Domain Constraint N text 20 Y 2 N Protein Domains constriant. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.
MA_GetAffy_GeneIntensity 15 display_columns Data Columns to Display N multioptionlist 4 Y Y N Desired data columns to display (or pivot) for the expression measurements "SELECT option_key,option_value FROM $TBMA_QUERY_OPTION WHERE option_type = 'GI_data_columns' ORDER BY sort_order,option_value"
MA_GetAffy_GeneIntensity 16 dbxref_tag_constraint Accession Number Database N multioptionlist 5 Y 2 N Database Name from for which there are accession numbers to: '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. "SELECT dbxref_tag, dbxref_tag FROM $TB_DBXREF"
MA_GetAffy_GeneIntensity 17 db_id_constraint Accession Number N text 10 Y 1 N Accession number to a foregin database
MA_GetAffy_GeneIntensity 18 genome_coordinates_constraint Genome Coordinates N text 50 Y Y N Specify the probe_set_ids 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 -
Current genome builds Human hg16
Mouse mm4
MA_GetAffy_GeneIntensity 19 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBMA_QUERY_OPTION WHERE option_type = 'GI_display_options' ORDER BY sort_order,option_value"
MA_GetAffy_GeneIntensity 20 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 10000 rows."
MA_affy_analysis 1 affy_analysis_id Affy Analysis ID int 4 0 N Y N N Y Affy Analysis ID
MA_affy_analysis 2 user_id User int 4 N Y optionlist 5 Y Y N User Name "SELECT user_login_id, username FROM $TB_USER_LOGIN WHERE record_status != 'D' ORDER BY username"
MA_affy_analysis 3 project_id Project int 4 N Y optionlist 5 Y Y N Project Name "SELECT project_id, username||' - '||name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN US ON ( P.PI_contact_id=US.contact_id ) WHERE P.project_id IN ( $accessible_project_ids ) ORDER BY username"
MA_affy_analysis 4 folder_name Folder Name varchar 50 N Y text 50 Y Y N "Folder that contains the analysis. There should be no need to change, but if you have to please make sure you know what you are doing."
MA_affy_analysis 5 parent_analysis_id Parent Analysis ID int 4 Y N text 10 Y Y N Parent analysis ID
MA_affy_analysis 6 affy_analysis_type_id Affy Analysis Type Name int 4 N MA_affy_analysis_type affy_analysis_type_id Y optionlist 5 Y Y N Type of analysis "SELECT aat.affy_analysis_type_id, aat.affy_analysis_name FROM $TBMA_AFFY_ANALYSIS_TYPE aat"
MA_affy_analysis 7 user_description User Description varchar 255 Y N textarea 4 Y Y N User Description about about the analysis. Please describe why this analysis was done.
MA_affy_analysis 8 analysis_description Analysis Description text 0 0 Y N textarea 4 Y Y N Computer generated descripition about what was done
MA_affy_analysis 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_analysis 6 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N Y
MA_affy_analysis 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_analysis 8 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N Y
MA_affy_analysis 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y
MA_affy_analysis 10 record_status Record Status char 1 0 N N N N N N
MA_affy_analysis_type 1 affy_analysis_type_id Affy Analysis ID int 4 0 N Y N N Y Affy Analysis Type ID
MA_affy_analysis_type 2 affy_analysis_name Affy Analysis Name varchar 50 0 N N Y text 30 Y Y N Affy Analysis type Name
MA_affy_analysis_type 3 affy_analysis_description Affy Analysis Description varchar 255 0 Y N N textarea 4 Y Y N Affy analysis description
MA_affy_analysis_type 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_analysis_type 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N Y
MA_affy_analysis_type 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N
MA_affy_analysis_type 7 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N Y
MA_affy_analysis_type 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y
MA_affy_analysis_type 9 record_status Record Status char 1 0 N N N N N N
MA_experiment_information 1 experiment_information_id Experiment Information ID int 4 0 N Y N N pkDEFAULT
MA_experiment_information 2 project_id Project ID int 4 0 N N project project_id Y optionlist Y Y Y Project with which this experiment is associated "SELECT project_id, username||' - '||name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN US ON ( P.PI_contact_id=US.contact_id ) WHERE project_id IN ( $accessible_project_ids ) AND P.record_status != 'D' ORDER BY name"
MA_experiment_information 3 name Name varchar 255 0 N N Y text 50 Y Y N Name of this Experiment Information
MA_experiment_information 4 tag Experiment Tag varchar 50 0 N N Y text 20 Y Y Y Shortened Name of this Experiment Information
MA_experiment_information 5 xml_file XML File varchar 255 0 N N Y file 40 Y Y N Experiment XML File
MA_experiment_information 6 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments
MA_experiment_information 7 sort_order Sort Order int 4 0 N 10 N N N N
MA_experiment_information 8 date_created Date Record Created datetime 4 0 N CURRENT_TIMESTAMP N N N
MA_experiment_information 9 created_by_id Record Created By int 4 0 N N contact contact_id N N
MA_experiment_information 10 date_modified Date Record Modified datetime 4 0 N CURRENT_TIMESTAMP N N N
MA_experiment_information 11 modified_by_id Record Modified By int 4 0 N N contact contact_id N N
MA_experiment_information 12 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_experiment_information 13 record_status Record Status char 1 0 N N N N N
MA_experiment_constants 1 experiment_constants_id Experiment Constants ID int 4 0 N Y N N pkDEFAULT
MA_experiment_constants 2 project_id Project ID int 4 0 N N project project_id Y optionlist Y Y Y Project with which this experiment is associated "SELECT project_id, username||' - '||name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN US ON ( P.PI_contact_id=US.contact_id ) WHERE project_id IN ( $accessible_project_ids ) AND P.record_status != 'D' ORDER BY name"
MA_experiment_constants 3 name Name varchar 255 0 N N Y text 50 Y Y N Name of this Constants File
MA_experiment_constants 4 tag Constants Tag varchar 50 0 N N Y text 20 Y Y Y Shortened Name of this Constants File
MA_experiment_constants 5 constants_file Constants File varchar 255 0 N N Y file 40 Y Y N Constants File Path
MA_experiment_constants 6 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments
MA_experiment_constants 7 sort_order Sort Order int 4 0 N 10 N N N N
MA_experiment_constants 8 date_created Date Record Created datetime 4 0 N CURRENT_TIMESTAMP N N N
MA_experiment_constants 9 created_by_id Record Created By int 4 0 N N contact contact_id N N
MA_experiment_constants 10 date_modified Date Record Modified datetime 4 0 N CURRENT_TIMESTAMP N N N
MA_experiment_constants 11 modified_by_id Record Modified By int 4 0 N N contact contact_id N N
MA_experiment_constants 12 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N
MA_experiment_constants 13 record_status Record Status char 1 0 N N N N N