Page History

ExpandtitleFull SEND ts.xpt FOR REFERENCE

This example Trial Sets dataset shows information about the test conditions for set A1 and A2 in this example study. Sets A1 and A2 can be seen in the first and second rows respectively of the sample report Table 1 (above). For brevity, the TX dataset and the findings (GT) dataset do not show information for any other sets. Fully formed datasets for this example study would include information about the test conditions and findings for all sets. 

Red font (CT is coming!, POSITIVE CONTROL, VEHICLE CONTROL, etc.)

ARMCD.      TREATMENT (element).       SETCD

ARM01             TREATMT.                                CS-01. (Cigarette Smoke 10 ug/mL)

ARM01

TA.XPT

TRIAL ARMS

TE.XPT

TRIAL ELEMENTS

tx.spt

TRIAL SET

example: Each plate has a separate product

Product, Smoking Regime (e.g. Traditional combustible, ENDS), Smoke Fraction, etc.

https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=969610#null

One study (Original sample of TK6 cells);  (6 rows in GT)
   

                 Assay (MNT) (ran on 10 tobacco products)
                      3 assay/test conditions; 
                             Treatment duration (2: ST, LT);
                             Presence of metabolic activation (2: presence, type)

                                    Concentrations of product (6 of these: 0, x, y, z,..., +CNTL);
                                    CytoTox % (3 different percentages from testing 1 portion of the original sample)
                                                4 MN counts conducted (on 4 different portions of original sample?)

EID (5 of these, Count1 - Count4 and Cytotox): with many TX Parm codes

Cytotox: RICC, RIC, RPD,  #cells

Dataset wrap
Name tx
Rowcaps Rows 1-23: Show trial set parameters and values that comprise the test conditions for trial set A1. Set A1 is the data for the negative control (concentration 0) with short-term exposure and metabolic activation S9.  The applicant has chosen to given a long name (SET) equal to "ST+S9_C0". Set A1 is associated with the first row in the sample report table for study 123. Rows 24-46: Show trial set parameters and values that comprise the test conditions for trial set A2. Set A2 is the data for the short-term exposure with metabolic activation S9 at a concentration of 1250 ug/ml. The applicant has chosen to give the set a long name (SET) equal to "ST+S9_C1250". Set A2 is associated with the second row in the sample report table for study 123. Dataset2 Row STUDYID DOMAIN TSSEQ SETCD TSGRPID SET TSPARMCD TXSEQ TSPARM TXPARMCD TSVAL TXPARM TSVALNF TXVAL 1 TS 123 TX A1 ST+S9_C0 1 SSTYP Study Type REPEAT DOSE TOXICITY 2 TS 1 SPECIES Species RAT 3 TS 1 STRAIN Strain/Substrain FISCHER 344 4 TS 1 SPLRNAM Test Subject Supplier HARLAN 5 TS 1 SDESIGN Study Design CROSSOVER 6 TS 1 ROUTE Route of Administration ORAL 7 TS 1 GLPTYP Good Laboratory Practice Type FDA 8 TS 1 EXPSTDTC Experimental Start Date 2008-01-01 9 TS 1 EXPENDTC Experimental End Date 2008-03-07 10 TS 1 TRMSAC Time to Terminal Sacrifice P42D 11 TS 1 STSTDTC Study Start Date 2007-12-30 12 TS 1 DOSDUR Dosing Duration P42D 13 TS 1 STITLE Study Title Example of a Crossover study in the Rat with 3 dose levels and 3 dosing periods 14 TS 1 SNDIGVER SEND Implementation Guide Version SEND IMPLEMENTATION GUIDE VERSION 3.2 15 TS 1 SNDCTVER SEND Controlled Terminology Version SEND Terminology 2021-03-26 16 TS 1 STCAT Study Category TOX 17 TS 1 SSPONSOR Sponsor Organization Example Sponsor Inc. 18 TS 1 SPREFID Sponsor's Study Reference ID NOT APPLICABLE 19 TS 1 1 TSTFNAM Test Facility Name Example Tox Lab Name 20 TS 1 1 TSTFLOC Test Facility Location 10 Somewhere Street, Montgomery, AL 10000 21 TS 1 1 TFCNTRY Test Facility Country USA 22 TS 1 AGETXT Age Text 6-8 23 TS 1 AGEU Age Unit WEEKS 24 TS 1 1 STDIR Study Director Dr. R. Smith 25 TS 1 TRT Investigational Therapy or Treatment Drug A 26 TS 1 2 TRTV Treatment Vehicle Saline 27 TS 1 2 TRTVDESC Treatment Vehicle Structured Description 100.46 %(w/v) ISOTONIC SODIUM CHLORIDE SOLUTION {UNII VR5Y7PDT5W} 28 TS 1 GLPFL GLP Flag Y 29 TS 1 TRTCAS Primary Treatment CAS Registry Number TEMPORARILY UNAVAILABLE Expand
Expand
title ta.xpt (trial arms)
Row	STUDYID	ASSAYID	DOMAIN	ARMCD	ARM	TAETORD	ETCD	ELEMENT
1	TA	ARM01-Prod1	Cigarette Smoke Condensate, 10 ug/mL	1	TREATMT	Treatment	9	9	SLS-110	1
Expand
title te.xpt (trial elements)
Row	STUDYID	ASSAYID	DOMAIN	ETCD	ELEMENT
TE	TREATMT	Treatment
Expand
title tx.xpt (trial sets)
Expand
title TX Domain
Row	STUDYID	ASSAYID	DOMAIN	ARMCD	ARM	TAETORD	ETCD	ELEMENT
1	TA	ARM01-Prod1	Cigarette Smoke Condensate, 10 ug/mL	1	TREATMT	Treatment	2	TA	ARM02-Prod1	Cigarette Smoke Condensate, 50 ug/mL	1	TREATMT	Treatment	3	TA	ARM03-Prod1	Cigarette Smoke Condensate, 75 ug/mL	1	TREATMT	Treatment	4	TA	4	1	5	TA	5	1	6	TA	6	1	7	7	1	8	8	1	9	9	SLS-110	1	10	ARM10	SLS-200	1
Row	STUDYID	ASSAYID	DOMAIN	ETCD	ELEMENT
TE	TREATMT	Treatment
Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	123	1	TX	METACT	Metabolic Activation	+S9	2	METACT	Metabolic Activation	-S9	TRTDUR	Treatment Duration	Short Term	TRTDUR	Treatment Duration	Long Term (or 2 parm codes, # and unit)	PRDCONC	Concentration of product	0	PRDCONCU	Concentration Unit	ug/ml	Product	Product Name	Smoking Regime	Smoke Fraction	TX	CS-10	Cigarette Smoke Condensate, 10 ug/mL	ARMCD	Arm Code	CS-10	TX	CS-10	Cigarette Smoke Condensate, 10 ug/mL	SPECIES	Species	Salmonella enterica	TX	CS-10	Cigarette Smoke Condensate, 10 ug/mL	STRAIN	Strain/Substrain	Salmonella enterica enterica	TX	CS-10	Cigarette Smoke Condensate, 10 ug/mL	PRODUCT	Product	product A	TX	CS-10	Cigarette Smoke Condensate, 10 ug/mL	REGIME	Smoking Regime	Traditional combustible	TX	CS-20	Cigarette Smoke Condensate, 50 ug/mL	ARMCD	Arm Code	CS-20	TX	CS-20	Cigarette Smoke Condensate, 50 ug/mL	PRODUCT	Product	product A	...	TX	LSL-200	sodium lauryl sulphate (SLS) positive control, 200 ug/mL	TRTDOS	Dose Level	100	TX	LSL-200	sodium lauryl sulphate (SLS) positive control, 200 ug/mL	TCNTRL	Control Type	POSITIVE CONTROL	TX	LSL-200	sodium lauryl sulphate (SLS) positive control, 200 ug/mL	CNTLAG	Control Agent	SODIUM LAURYL SULPHATE	TX	LSL-200	sodium lauryl sulphate (SLS) positive control, 200 ug/mL	CNTLAGAMT	Control Agent amount (levels)	110	LSL-200	sodium lauryl sulphate (SLS) positive control, 200 ug/mL	CNTLAGUNIT	Control Agent Unit	ug/mL
Expand
title ei.xpt (dm-like)
Row	STUDYID	DOMAIN	ENID (Entity ID)	RICC	RCC	RPD	Sum of cell ev.	Cells with MN	SMKFID (Smoke Fraction)	REPLCTID (Replicate Number)	PLATEID (Plate ID)	COLID (Column number)	ROWID (Row  number)	SETCD (Set Code, TX)	RFSTDTC	RFENDTC	RFXSTDTC	RFXENDTC	RFCSTDTC	RFCENDTC	ARMCD	1	MA99999	GT	030001	A	1	1	1	A	CS-10	2008-04-01T06:00	2008-04-28T14:00	2008-04-02T14:00	2008-04-02T14:04	2008-04-01T06:00	2008-04-01T06:00	3	2	MA99999	GT	1	1-1	030001	A	1	1	1	B	CS-10	2008-04-01T06:00	2008-04-21T14:00	2008-04-02T20:00	2008-04-02T20:04	2008-04-01T06:00	2008-04-01T06:00	3	2	3	4

Expand
title Notes for creating GT domain
Entity ID links to EI domain (usubjid) TEST:  After ST exposure to increasing concentrations of test article in the presence of S9 mix

MTACTIND Metabolic Activating Agent Name +S9 2 123 TX A1 ST+S9_C0 2 METACTFL Presence of Metabolic Activation Flag Y 3 123 TX A1 ST+S9_C0 3 IVTDMIN In vitro Treatment Duration Minimum 3 4 123 TX A1 ST+S9_C0 4 IVTDTRG In vitro Treatment Duration Target 3.5 5 123 TX A1 ST+S9_C0 5 IVTDMAX In vitro Treatment Duration Maximum 4 6 123 TX A1 ST+S9_C0 6 IVTDU In vitro Treatment Duration Unit HOURS 7 123 TX A1 ST+S9_C0 7 RCVDMIN Recovery Duration Minimum 23.5 8 123 TX A1 ST+S9_C0 8 RCVDTRG Recovery Duration Target 24 9 123 TX A1 ST+S9_C0 9 RCVDMAX Recovery Duration Maximum 24.5 10 123 TX A1 ST+S9_C0 10 RCVDU Recovery Duration Unit HOURS 11 123 TX A1 ST+S9_C0 11 INCBTMP Incubation Temperature 37 12 123 TX A1 ST+S9_C0 12 INCBTMPU Incubation Temperature Unit C 13 123 TX A1 ST+S9_C0 13 ATMRHP Atmospheric Relative Humidity Percent 50 14 123 TX A1 ST+S9_C0 14 ATMCO2P Atmospheric CO2 Percent 5 15 123 TX A1 ST+S9_C0 15 SPTOBID Applicant-defined tobacco identifier CIG01a 16 123 TX A1 ST+S9_C0 16 EXPTYP Exposure Type Submerged 17 123 TX A1 ST+S9_C0 17 SAMTYP Sample Type Total Particulate Matter in DMSO 18 123 TX A1 ST+S9_CO 18 ITVNAM Intervention Article Name Tobacco ProdA 19 123 TX A1 ST+S9_C0 19 ITVTYPE Intervention Article Type Negative Control 20 123 TX A1 ST+S9_C0 20 ITVCONC Intervention Article Concentration 0 21 123 TX A1 ST+S9_C0 21 ITVCONCU Intervention Article Concentration Unit ug/ml 22 123 TX A1 ST+S9_C0 22 SPDEVID Applicant-defined device identifier PUFFMASTER3K 23 123 TX A1 ST+S9_C0 23 SMKRGM Smoking Regimen MEDIUM INTENSITY REGIMEN 24 123 TX A2 ST+S9_C1250 24 MTACTIND Metabolic Activating Agent Name +S9 25 123 TX A2 ST+S9_C1250 25 METACTFL Presence of Metabolic Activation Flag Y 26 123 TX A2 ST+S9_C1250 26 IVTDMIN In vitro Treatment Duration Minimum 3 27 123 TX A2 ST+S9_C1250 27 IVTDTRG In vitro Treatment Duration Target 3.5 28 123 TX A2 ST+S9_C1250 28 IVTDMAX In vitro Treatment Duration Maximum 4 29 123 TX A2 ST+S9_C1250 29 IVTDU In vitro Treatment Duration Unit HOURS 30 123 TX A2 ST+S9_C1250 30 RCVDMIN Recovery Duration Minimum 23.5 31 123 TX A2 ST+S9_C1250 31 RCVDTRG Recovery Duration Target 24 32 123 TX A2 ST+S9_C1250 32 RCVDMAX Recovery Duration Maximum 24.5 33 123 TX A2 ST+S9_C1250 33 RCVDU Recovery Duration Unit HOURS 34 123 TX A2 ST+S9_C1250 34 INCBTMP Incubation Temperature 37 35 123 TX A2 ST+S9_C1250 35 INCBTMPU Incubation Temperature Unit C 36 123 TX A2 ST+S9_C1250 36 ATMRHP Atmospheric Relative Humidity Percent 50 37 123 TX A2 ST+S9_C1250 37 ATMCO2P Atmospheric CO2 Percent 5 38 123 TX A2 ST+S9_C1250 38 SPTOBID Applicant-defined tobacco identifier CIG01a 39 123 TX A2 ST+S9_C1250 39 EXPTYP Exposure Type Submerged 40 123 TX A2 ST+S9_C1250 40 SAMTYP Sample Type Total Particulate Matter in DMSO 41 123 TX A2 ST+S9_C1250 41 ITVNAM Intervention Article Name Tobacco ProdA 42 123 TX A2 ST+S9_C1250 42 ITVTYPE Intervention Article Type Product 43 123 TX A2 ST+S9_C1250 43 ITVCONC Intervention Article Concentration 1250 44 123 TX A2 ST+S9_C1250 44 ITVCONCU Intervention Article Concentration Unit ug/ml 45 123 TX A2 ST+S9_C1250 45 SPDEVID Applicant-defined Device Identifier PUFFMASTER2023 46 123 TX A2 ST+S9_C1250 46 SMKRGM Smoking Regimen HIGH INTENSITY REGIMEN

Dataset wrap
Name relref
Rowcaps Row 1: Shows the value of REFID=C0. This REFID refers to the trial set with a SETCD of "A1", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set. Rows 2-5: Show the values of 4 observational units (C0_Count1 through C0_Count4) that are within the parent experimental unit, REFID=C0. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset. Row 6: Shows the value of REFID=C1250. This REFID refers to the trial set with a SETCD of "A2", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set. Rows 7-10: Show the values of 4 observational units (C1250_Count1 through C1250_Count4) that are within the parent experimental unit, REFID=C1250. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset. Dataset2 tableid relref Row STUDYID SETCD REFID PARENT LEVEL LVLDESC 1 123 A1 C0 1 EXPERIMENTAL UNIT/TRIAL SET 2 123 A1 C0-Count1 C0 2 OBSERVATIONAL UNIT 3 123 A1 C0-Count2 C0 2 OBSERVATIONAL UNIT 4 123 A1 C0-Count3 C0 2 OBSERVATIONAL UNIT 5 123 A1 C0-Count4 C0 2 OBSERVATIONAL UNIT 6 123 A2 C1250 1 EXPERIMENTAL UNIT/TRIAL SET 7 123 A2 C1250-Count1 C1250 2 OBSERVATIONAL UNIT 8 123 A2 C1250-Count2 C1250 2 OBSERVATIONAL UNIT 9 123 A2 C1250-Count3 C1250 2 OBSERVATIONAL UNIT 10 123 A2 C1250-Count4 C1250 2 OBSERVATIONAL UNIT

ug/mL

Dataset wrap
Name gt
Rowcaps Rows 1-3, 8: Show percentage result values that apply to GTREFID=C0. REFID=C0, as shown in the RELREF dataset, relates this data to the trial set in the first row of table 1 in the sample report table for study 123. Rows 4-7: Show the 4 micronucleated cell counts for the observational units with GTREFID from C0-Count1 through C0-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset. Rows 9-11, 16: Show percentage result values that apply to GTREFID=C1250. REFID=C1250, as shown in the RELREF dataset, relates this data to the trial set in the second row of table 1 in the sample report table for study 123. Rows 12-15: Show the 4 micronucleated cell counts for the observational units with GTREFID from C1250-Count1 through C1250-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset. Dataset2 Row STUDYID DOMAIN GTSEQ GTREFID GTTESTCD GTTEST GTCELLEV GTORRES GTORRESU GTCOLSRT GTSTRESC GTSTRESN GTSTRESU GTDTC 1 123 GT 1 C0 RICC Relative Increase in Cell Count 154 0 % 0 0 % 2022-05-25 2 123 GT 2 C0 RCC Relative Cell Count 154 0 % 0 0 % 2022-05-25 3 123 GT 3 C0 RPD Relative Population Doubling 154 0 % 0 0 % 2022-05-25 4 123 GT 4 C0-Count1 MNCE Micronucleated Cells 2205 15 15 15 2022-05-25 5 123 GT 5 C0-Count2 MNCE Micronucleated Cells 2474 13 13 13 2022-05-25 6 123 GT 6 C0-Count3 MNCE Micronucleated Cells 2758 17 17 17 2022-05-25 7 123 GT 7 C0-Count4 MNCE Micronucleated Cells 2669 12 12 12 2022-05-25 8 123 GT 8 C0 MNCECE Micronucleated Cells/Total Cells 0.57 % 0.57 0.57 % 2022-05-25 9 123 GT 1 C1250 RICC Relative Increase in Cell Count 134 15.7 % 15.7 15.7 % 2022-05-25 10 123 GT 2 C1250 RCC Relative Cell Count 134 13.0 % 13.0 13.0 % 2022-05-25 11 123 GT 3 C1250 RPD Relative Population Doubling 134 7.9 % 7.9 7.9 % 2022-05-25 12 123 GT 4 C1250-Count1 MNCE Micronucleated Cells 3266 20 20 20 2022-05-25 13 123 GT 5 C1250-Count2 MNCE Micronucleated Cells 2190 17 17 17 2022-05-25 14 123 GT 6 C1250-Count3 MNCE Micronucleated Cells 2758 13 13 13 2022-05-25 15 123 GT 7 C1250-Count4 MNCE Micronucleated Cells 2714 21 21 21 2022-05-25 16 123 GT 8 C1250 MNCECE Micronucleated Cells/Total Cells 0.66 % 0.66 0.66 % 2022-05-25
Expand
title gt.xpt (similar to LB)
	Row	STUDYID	DOMAIN	TXCD	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU	GTCELLEV (cells evaluated)	GTSPEC???	GTMETHOD	GTDTC	GTDY	GTNOMDY	GTELTM	GTTPTREF	1	ST487-12	GT	RICC	ug/mL	ug/mL	25-05-2022	2	ST487-12	GT	RCC	ug/mL	ug/mL	3	ST487-12	GT	RPD	ug/mL	ug/mL	4	ST487-12	GT	CELLS	Sum of cells evaluated	ug/mL	ug/mL	5	ST487-12	GT	MNNUM	Cells with Micronuclei	ug/mL	ug/mL	6	ST487-12	GT	MNT	In vitro Micronucleus Assay	ug/mL	ug/mL	7	ST487-12	GT	MNT	In vitro Micronucleus Assay	ug/mL	ug/mL	8	ST487-12	GT	MNT	In vitro Micronucleus Assay	ug/mL	ug/mL	9	ST487-12	GT	MNT	In vitro Micronucleus Assay	ug/mL