Page History

populate units of COLONIES
recreate the data table - clean up, add "S" to the first set A
move assumptions out of all of the examples
add row captions to highlight exceptions/assumptions

This is an example showing the report table, trial design, and results from the a study's in vitro bacterial reverse mutation test of Study #8325064. The bacterial reverse mutation test uses using 4 different amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and Escherichia coli ( and 1 strain of E. coli) to detect point mutations, which involve substitution, addition or deletion of one or a few DNA base pairs. The principle of this bacterial reverse mutation test is that it detects chemicals that induce mutations which revert mutations present in the tester strains and restore the functional capability of the bacteria to synthesize an essential amino acid. The revertant bacteria are detected by their ability to grow in the absence of the amino acid required by the parent tester strain.

Image Removed

...

title	ts.xpt (trial summary, study level parameters)

Assumption: When the experimental unit is derived from the species and strain, such as a cell line, then TESTSYS should be supplied.

...

Row

...

STUDYID

...

DOMAIN

...

TSSEQ

...

TSGRPID

...

TSPARMCD

...

TSPARM

...

TSVAL

...

TSVALNF

...

1

...

2

...

3

...

4

...

The Bacterial Reverse Mutation Test, Study 8325064-1

...

5

...

6

...

7

...

8

...

9

...

10

...

.

Expand

title	Report Table for Example Study 8325064

This table shows the assay results for study 8325064, test article TA1, and 3 strains of salmonella (TA98, TA100, and TA1535) at varying concentrations. For brevity, the remaining tables (e.g., additional strains, samples prepared without metabolic activation) are not included. For ease of reference in the table below, each row has been labeled in the right-hand margin with the applicant-defined trial set label (e.g., SetA). For brevity, only the four bolded sets are represented in the following example datasets.

Image Added

This example Trial Summary (TS) dataset, shows many informational fields that provide context at the study level.

Dataset wrap

Rowcaps

Rows 1-2:	Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this study.
Row 3:	Shows that this study was conducted as a GLP study.
Rows 4-5:	Show the study start date and study title.
Rows 6-7:	Show the version of SEND Implementation Guide and version of Controlled Terminology used in this study.
Row 8:	Shows the applicant's organization.
Row 9:	Shows that the applicant's study reference ID is not applicable.
Rows 10-13:	Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID=1). The study director is associated with the test facility.
Rows 14-16:	Show that TSGRPID (TSGRPID=4) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER).
Row 17:	Shows the study type for this study.
Row 18:	Shows that this study includes a Bacterial Reverse Mutation Assay.
Rows 19-27:	Show that TSGRPID (TSGRPID = 2) has been used to link the information for 1 species (salmonella) with the 4 different strains and cell lines that are tested in this study.
Rows 28-30:	Show that TSGRPID (TSGRPID = 3) has been used to link the information for 1 species (E. coli) with the strain and cell line that is tested in this study.

Dataset2

Row	STUDYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	8325064	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	8325064	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	8325064	TS	1		GLPFL	GLP Flag	N
4	8325064	TS	1		STSTDTC	Study Start Date	2015-07-29
5	8325064	TS	1		STITLE	Study Title	The Bacterial Reverse Mutation Test, Study 8325064-1
6	8325064	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
7	8325064	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
8	8325064	TS	1		APPLCNT	Applicant	Example Applicant Inc.
9	8325064	TS	1		APREFID	Applicant's Study Reference ID		NOT APPLICABLE
10	8325064	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
11	8325064	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
12	8325064	TS	1	1	TFCNTRY	Test Facility Country	USA
13	8325064	TS	1	1	STDIR	Study Director	Dr. R. Smith
14	8325064	TS	1	4	TSTGDNAM	Testing Guideline Name	Test NO. 471
15	8325064	TS	1	4	TSTGDORG	Testing Guideline Organization	OECD
16	8325064	TS	1	4	TSTGDVER	Testing Guideline Version	2020-06-29
17	8325064	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
18	8325064	TS	1		GNTXAID	Genetic Toxicology Assay Identifier	AMES
19	8325064	TS	1	2	SPECIES	Species	SALMONELLA TYPHIMURIUM
20	8325064	TS	1	2	STRAIN	Strain/Substrain	TA98
21	8325064	TS	2	2	STRAIN	Strain/Substrain	TA100
22	8325064	TS	3	2	STRAIN	Strain/Substrain	TA1535
23	8325064	TS	4	2	STRAIN	Strain/Substrain	TA1537
24	8325064	TS	1	2	CELLLN	Cell Line	TA 98 hisD3052; rfa-; uvrB-
25	8325064	TS	2	2	CELLLN	Cell Line	TA 100 hisG46; rfa-; uvrB-
26	8325064	TS	3	2	CELLLN	Cell Line	TA 1535 hisG46; rfa-; uvrB-
27	8325064	TS	4	2	CELLLN	Cell Line	TA 1537 hisC3076; rfa-; uvrB-
28	8325064	TS	2	3	SPECIES	Species	ESCHERICHIA COLI
29	8325064	TS	5	3	STRAIN	Strain/Substrain	WP2 uvrA pKM101
30	8325064	TS	5	3	CELLLN	Cell Line	trpE uvrA

This example Trial Set (TX) dataset shows information about the test conditions for SetA and SetR in this study. For brevity, the dataset does not show information for SetF, SetG, or any other sets. A fully formed TX dataset for this example study would include information about the test conditions for all sets.

Note that there are three trial set parameters that link to other important datasets: SPTOBID, APDEVID, and SMKRGM.

SPTOBID (Applicant-Defined Tobacco Product ID) is used to uniquely identify the tobacco product. The value of SPTOBID (e.g., CIG01a) matches the value for SPTOBID in all the TOPARMCD-TOVAL pairs in the Tobacco Product Identifiers and Descriptors (TO) dataset example in Section 3.1.2, Product Design Parameters and Conformance Testing, Example 1. The TOPARMCD-TOVAL pairs identify this unique product, CIG01a. The TO domain is described in Section 2.8.8.1, Tobacco Product Identifiers and Descriptors (TO).
The value of APDEVID (e.g., PUFFMASTER3K) matches the value of SPDEVID in all the DIPARMCD-DIVAL pairs that identify this unique device in the DI dataset. SPDEVID is the applicant-defined device identifier that is used to uniquely identify the device in the Unique Device Identification (DI) dataset (see also Section 2.8.9.7, SEND Device Identifiers (DI)). This is shown in the DI dataset in Section 3.1.3.2, HPHCs, Other Constituents, and Smoking/Vaping Regimens, Example 1.
SMKRGM serves as a link to the Device-In Use Properties (DU) domain (see also Section 2.8.9.8, SEND Device-In-Use (DU)), where a matching value of SMKRGM indicates parameters of the smoking regimen performed by the smoking machine, as in the DU dataset in Section 3.1.3.2, HPHCs, Other Constituents, and Smoking/Vaping Regimens, Example 2.

Dataset wrap

Name	tx

Rowcaps

Rows 1-22:	Show trial set parameters and trial set values that are the test conditions specific to set SetA which is the vehicle control (i.e., Strain of TA98, vehicle control with concentration value of 0). SetA is associated with the first row, labeled "SetA", in the report table for example study 8325064.
Rows 23-44:	Show trial set parameters and trial set values that comprise the test conditions for the set SetF which is the strain of TA98 with a concentration value of 500 µg/plate. SetF is associated with the sixth row, labeled "SetF", in the report table for example study 8325064.
Rows 45-66:	Show trial set parameters and trial set values that comprise the test conditions for the set SetG which is the strain of TA98 with a concentration value of 1600 µg/plate. SetG is associated with the seventh row, labeled "SetG", in the report table for example study 8325064.
Rows 67-88:	Show trial set parameters and trial set values that comprise the test conditions for the set SetR which is the strain of TA100, positive control with a concentration value of 2 µg/plate. SetR is associated with the eighteenth row, labeled "SetR", in the report table for example study 8325064.

Dataset2

Row	STUDYID	DOMAIN	SETCD	SET	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	8325064

...

11

...

12

...

13

...

14

...

15

...

16

...

17

...

18

...

19

...

20

...

21

...

22

...

23

...

24

...

Expand

title	Raw Data Table for Study 8325064

Image Removed

How do we handle "toxic, no revertant colonies"? (LAK will add 6 records with GTSTAT = NOT DONE, GTREASND = "TOO MUCH CYTOTOXICITY,"
Condition of background bacterial lawn? Slight thinning, Very thin? - refer to SEND team's marked-up table.
- new Test code of Cytotoxicity with GTORRES = S, V (controlled terms)
- Each plate we would have one result record for Revertent count and another for the lawn evaluation (NORMAL, SLIGHT THINNING, VERY THIN)
When "-" in Mean, Std Dev, Fold Inc - refer to SEND team's marked-up table (GTSTAT = NOT DONE; variety of REASND)

Ames

Dataset wrap

Name	tx.xpt Trial Sets

Rowcaps

Rows 1-22:

Shows trial set parameters and trial set values that comprise the test conditions for the set SetA. SetA is the first row of the raw data table, see the row labeled "SetA" in the table, Raw Data for Study 8325064.

Rows 2-4:

Show two records for Alkaline Phosphatase that were collected 1 day apart and are expected to be reported together. Row 4 shows how to create a derived record (average of the Rows 2 and 3) and flag it as Derived (LBDRVFL = "Y") as well as the record to use as baseline (LBBLFL = "Y").

Rows 6-7:

Show a suggested use of the LBSCAT variable. It could be used to further classify types of tests within a laboratory panel (e.g., "DIFFERENTIAL").

Row 9:

Shows the proper use of the LBSTAT variable to indicate "NOT DONE," when the fact that the test was done was documented.

Row 12:

The subject had Cholesterol measured. The normal range for this test is <200 mg/dL. The value <200 may not be used in the normal range variables LBORNRHI or LBSTNRHI; however, a sponsor may decide, e.g., to enter "0" into LBORNRLO and "199" in LBORNRHI. The sponsor must define the appropriate value for all of the normal range variables.

Row 13:

Shows the use of LBUSCHFL to indicate that the test result was obtained from an unscheduled blood collection. In this case, the subject was moribund and a blood sample was taken prior to sacrifice.

Rows 1, 6:

Use records in the SUPPLB dataset example to show biological significance assigned by the investigator for test results.

Expand

title	tx.xpt (trial sets)

Row

STUDYID

ASSAYID

DOMAIN

SETCD

SET

TXSEQ

TXPARMCD

TXPARM

TXVAL

1

8325064

Ames

TX

SetA

A-TA98-C0

1

SPECIES

Species

Salmonella typhimurium

2

8325064

Ames

TX

SetA

A-TA98-C0

2

STRAIN

Strain/Substrain

TA98

3

8325064

Ames

TX

SetA

A-TA98-C0

3

METACT

Metabolic Activation

4

8325064

Ames

TX

SetA

A-TA98-C0

4

METACTFL

Y/N presence of metabolic activation

N

5

8325064

Ames

TX

SetA

A-TA98-C0

5

TRTDMIN

Treatment Duration Minimum

71.5

6

8325064

Ames

TX

SetA

A-TA98-C0

6

TRTDTRG

Treatment Duration Target

72

7

8325064

Ames

TX

SetA

A-TA98-C0

7

TRTDMAX

Treatment Duration Maximum

72.5

8

8325064

TX

SetA

A-TA98-C0

8

1

TRTDU

SPECIES

Treatment Duration UnitHOURS

Species	SALMONELLA TYPHIMURIUM
2

9

8325064

Ames

TX

SetA

A-TA98-C0

9

2

INCBTMPIncubation Temperature37

IVTDMIN	In vitro Treatment Duration Minimum	71.5
3

10

8325064

Ames

TX

SetA

A-TA98-C0

10

3

INCBTMPUIncubation Temperature UnitC

IVTDTRG	In vitro Treatment Duration Target	72
4

11

8325064

Ames

TX

SetA

A-TA98-C0

11

4

HUMIDAtmospheric Relative Humidity Percent50

IVTDMAX	In vitro Treatment Duration Maximum	72.5
5	8325064

128325064Ames

TX

SetA

A-TA98-C0

12

5

ATMCO2Atmospheric CO2 Percent5138325064

IVTDU	In vitro Treatment Duration Unit	HOURS
6	8325064

Ames

TX

SetA

A-TA98-C0

13

6

SPTOBID

Sponsor defined tobacco identifier

CIG01a

INCBTMP	Incubation Temperature	37
7

14

8325064

Ames

TX

SetA

A-TA98-C0

14EXPTYP

Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)

Submerged158325064Ames

	7	INCBTMPU	Incubation Temperature Unit	C
8	8325064

TX

SetA

A-TA98-C0

15

8

SAMTYP

Sample Type

Total Particulate Matter in PBS

ATMRHP	Atmospheric Relative Humidity Percent	50
9

16

8325064

Ames

TX

SetA

A-TA98-C0

16

9

INTRVN

name of the intervention article

TA1

ATMCO2P	Atmospheric CO2 Percent	5
10

17

8325064

Ames

TX

SetA

A-TA98-C0

17

10

ITVTYPE

type of intervention article

Vehicle Control188325064

SPTOBID	Applicant-defined tobacco identifier	CIG01a
11	8325064

Ames

TX

SetA

A-TA98-C0

18

11

ITVCONCConcentration of intervention article0

EXPTYP	Exposure Type	Submerged
12

19

8325064

Ames

TX

SetA

A-TA98-C0

19

12

ITVCONCU

SAMTYP

Concentration Unitug/plate

Sample Type	Total Particulate Matter in PBS
13	8325064

208325064Ames

TX

SetA

A-TA98-C0

20

13

TRTVTreatment VehicleDMSO

APDEVID	Applicant-defined device identifier	PUFFMASTER3K
14

21

8325064

Ames

TX

SetA

A-TA98-C0

21

14

SPDEVIDSponsor defined device identifierPUFFMASTER3K

SMKRGM	Smoking Regimen	NON-INTENSE REGIMEN
15	8325064

228325064Ames

TX

SetA

A-TA98-C0

22

15

DUREFIDSmoke RegimenMedium Intensity Regimen

STRAIN	Strain/Substrain	TA98
16

23

8325064

Ames

TX

SetF

(row 6)

SetA

A

F

-TA98-

C500

C0

16

1SPECIESSpecies

MTACTIND	Metabolic Activating Agent Name	NOT APPLICABLE
17

24

8325064

Ames

TX

SetF

SetA

F

A-TA98-

C500

C0

17

2STRAINStrain/Substrain

METACTFL	Presence of Metabolic Activation Flag	N
18

25

8325064

Ames

TX

SetF

SetA

F

A-TA98-

C500

C0

3METACTMetabolic Activation

18	ITVNAM	Intervention Article Name	DMSO
19

26

8325064

Ames

TX

SetF

SetA

F

A-TA98-

C500

C0

4

19

METACTFLY/N presence of metabolic activationN

ITVTYPE	Intervention Article Type	VEHICLE
20

27

8325064

Ames

TX

SetF

SetA

F

A-TA98-

C500TRTDRTOLTreatment Duration Tolerance288325064

C0	20	ITVCONC	Intervention Article Concentration	100
21	8325064

Ames

TX

SetF

SetA

F

A-TA98-

C500

C0

TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)

21	ITVCONCU	Intervention Article Concentration Unit	%
22	8325064	TX	SetA	A-TA98-C0	22	TRTV	Treatment Vehicle	DMSO
23	8325064

8325064Ames

TX

SetF

F-TA98-C500

INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

TA18325064

23	SPECIES	Species	SALMONELLA TYPHIMURIUM
24	8325064

Ames8325064Ames

TX

SetF

F-TA98-C500

ITVTYPE

type of intervention article

choices of values: product; negative control; positive control

Product

24	IVTDMIN	In vitro Treatment Duration Minimum	71.5
25	8325064

TX

SetF

F-TA98-C500

ITVCONCConcentration of intervention article

	25	IVTDTRG	In vitro Treatment Duration Target	72
26

500

8325064

Ames

TX

SetF

F-TA98-C500

ITVCONCUConcentration Unitug/plate8325064

	26	IVTDMAX	In vitro Treatment Duration Maximum	72.5
27	8325064

Ames

TX

SetF

F-TA98-C500

STRAIN

27

Strain/SubstrainTA988325064Ames

IVTDU	In vitro Treatment Duration Unit	HOURS
28	8325064	TX	SetF	F-TA98-C500

REGIMESmoking RegimeISO Regime...8325064AmesTX

SetG (row 7) do G not I!!!

METACTMetabolic Activation (should there be two parms? Presence, type)?None8325064AmesTXSetGTRTDRTRGTreatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)8325064AmesTXSetGTRTDRTOLTreatment Duration Tolerance8325064AmesTXSetGTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)8325064AmesTXSetGINTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

2-Nitrofluorine8325064AmesTXSetGITVTYPE

type of intervention article

choices of values: product; negative control; positive control

Positive Control8325064AmesTXSetGITVCONCConcentration of intervention article58325064AmesTXSetGITVCONCUConcentration Unitug/plate8325064AmesTXSetGREGIMESmoking RegimeISO...SetG8325064AmesTX

SetR

(Row 18)

METACTMetabolic Activation (should there be two parms? Presence, type)?None8325064AmesTX

SetR

TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)8325064AmesTXSetRTRTDRTOLTreatment Duration Tolerance8325064AmesTXSetRTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)8325064AmesTXSetRINTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

4-Nitroquinoline-1-oxide8325064AmesTXSetRITVTYPE

type of intervention article

choices of values: product; negative control; positive control

Positive Control8325064AmesTXSetRITVCONCConcentration of intervention article28325064AmesTXSetRITVCONCUConcentration Unitug/plate8325064AmesTXSetRSTRAINStrain/SubstrainTA988325064AmesTXSetRREGIMESmoking RegimeISO Dataset wrap

Name	ou.xpt Observational and Experimental Unit Identifiers

Rowcaps

28	INCBTMP	Incubation Temperature	37
29	8325064	TX	SetF	F-TA98-C500	29	INCBTMPU	Incubation Temperature Unit	C
30	8325064	TX	SetF	F-TA98-C500	30	ATMRHP	Atmospheric Relative Humidity Percent	50
31	8325064	TX	SetF	F-TA98-C500	31	ATMCO2P	Atmospheric CO2 Percent	5
32	8325064	TX	SetF	F-TA98-C500	32	SPTOBID	Applicant-defined tobacco identifier	CIG01a
33	8325064	TX	SetF	F-TA98-C500	33	EXPTYP	Exposure Type	Submerged
34	8325064	TX	SetF	F-TA98-C500	34	SAMTYP	Sample Type	Total Particulate Matter in PBS
35	8325064	TX	SetF	F-TA98-C500	35	APDEVID	Applicant-defined device identifier	PUFFMASTER3K
36	8325064	TX	SetF	F-TA98-C500	36	SMKRGM	Smoking Regimen	NON-INTENSE REGIMEN
37	8325064	TX	SetF	F-TA98-C500	37	STRAIN	Strain/Substrain	TA98
38	8325064	TX	SetF	F-TA98-C500	38	MTACTIND	Metabolic Activating Agent Name	NOT APPLICABLE
39	8325064	TX	SetF	F-TA98-C500	39	METACTFL	Presence of Metabolic Activation Flag	N
40	8325064	TX	SetF	F-TA98-C500	40	ITVNAM	Intervention Article Name	TA1
41	8325064	TX	SetF	F-TA98-C500	41	ITVTYPE	Intervention Article Type	PRODUCT
42	8325064	TX	SetF	F-TA98-C500	42	ITVCONC	Intervention Article Concentration	500
43	8325064	TX	SetF	F-TA98-C500	43	ITVCONCU	Intervention Article Concentration Unit	ug/plate
44	8325064	TX	SetF	F-TA98-C500	44	TRTV	Treatment Vehicle	DMSO
45	8325064	TX	SetG	G-TA98-C1600	45	SPECIES	Species	SALMONELLA TYPHIMURIUM
46	8325064	TX	SetG	G-TA98-C1600	46	IVTDMIN	In vitro Treatment Duration Minimum	71.5
47	8325064	TX	SetG	G-TA98-C1600	47	IVTDTRG	In vitro Treatment Duration Target	72
48	8325064	TX	SetG	G-TA98-C1600	48	IVTDMAX	In vitro Treatment Duration Maximum	72.5
49	8325064	TX	SetG	G-TA98-C1600	49	IVTDU	In vitro Treatment Duration Unit	HOURS
50	8325064	TX	SetG	G-TA98-C1600	50	INCBTMP	Incubation Temperature	37
51	8325064	TX	SetG	G-TA98-C1600	51	INCBTMPU	Incubation Temperature Unit	C
52	8325064	TX	SetG	G-TA98-C1600	52	ATMRHP	Atmospheric Relative Humidity Percent	50
53	8325064	TX	SetG	G-TA98-C1600	53	ATMCO2P	Atmospheric CO2 Percent	5
54	8325064	TX	SetG	G-TA98-C1600	54	SPTOBID	Applicant-defined tobacco identifier	CIG01a
55	8325064	TX	SetG	G-TA98-C1600	55	EXPTYP	Exposure Type	Submerged
56	8325064	TX	SetG	G-TA98-C1600	56	SAMTYP	Sample Type	Total Particulate Matter in PBS
57	8325064	TX	SetG	G-TA98-C1600	57	APDEVID	Applicant-defined device identifier	PUFFMASTER3K
58	8325064	TX	SetG	G-TA98-C1600	58	SMKRGM	Smoking Regimen	NON-INTENSE REGIMEN
59	8325064	TX	SetG	G-TA98-C1600	59	STRAIN	Strain/Substrain	TA98
60	8325064	TX	SetG	G-TA98-C1600	60	MTACTIND	Metabolic Activating Agent Name	NOT APPLICABLE
61	8325064	TX	SetG	G-TA98-C1600	61	METACTFL	Presence of Metabolic Activation Flag	N
62	8325064	TX	SetG	G-TA98-C1600	62	ITVNAM	Intervention Article Name	TA1
63	8325064	TX	SetG	G-TA98-C1600	63	ITVTYPE	Intervention Article Type	Product
64	8325064	TX	SetG	G-TA98-C1600	64	ITVCONC	Intervention Article Concentration	1600
65	8325064	TX	SetG	G-TA98-C1600	65	ITVCONCU	Intervention Article Concentration Unit	ug/plate
66	8325064	TX	SetG	G-TA98-C1600	66	TRTV	Treatment Vehicle	DMSO
67	8325064	TX	SetR	R-TA100-C2	67	SPECIES	Species	SALMONELLA TYPHIMURIUM
68	8325064	TX	SetR	R-TA100-C2	68	IVTDMIN	In vitro Treatment Duration Minimum	71.5
69	8325064	TX	SetR	R-TA100-C2	69	IVTDTRG	In vitro Treatment Duration Target	72
70	8325064	TX	SetR	R-TA100-C2	70	IVTDMAX	In vitro Treatment Duration Maximum	72.5
71	8325064	TX	SetR	R-TA100-C2	71	IVTDU	In vitro Treatment Duration Unit	HOURS
72	8325064	TX	SetR	R-TA100-C2	72	INCBTMP	Incubation Temperature	37
73	8325064	TX	SetR	R-TA100-C2	73	INCBTMPU	Incubation Temperature Unit	C
74	8325064	TX	SetR	R-TA100-C2	74	ATMRHP	Atmospheric Relative Humidity Percent	50
75	8325064	TX	SetR	R-TA100-C2	75	ATMCO2P	Atmospheric CO2 Percent	5
76	8325064	TX	SetR	R-TA100-C2	76	SPTOBID	Applicant-defined tobacco identifier	CIG01a
77	8325064	TX	SetR	R-TA100-C2	77	EXPTYP	Exposure Type	Submerged
78	8325064	TX	SetR	R-TA100-C2	78	SAMTYP	Sample Type	Total Particulate Matter in PBS
79	8325064	TX	SetR	R-TA100-C2	79	APDEVID	Applicant-defined device identifier	PUFFMASTER3K
80	8325064	TX	SetR	R-TA100-C2	80	SMKRGM	Smoking Regimen	NON-INTENSE REGIMEN
81	8325064	TX	SetR	R-TA100-C2	81	STRAIN	Strain/Substrain	TA100
82	8325064	TX	SetR	R-TA100-C2	82	MTACTIND	Metabolic Activating Agent Name	NOT APPLICABLE
83	8325064	TX	SetR	R-TA100-C2	83	METACTFL	Presence of Metabolic Activation Flag	N
84	8325064	TX	SetR	R-TA100-C2	84	ITVNAM	Intervention Article Name	NaN3
85	8325064	TX	SetR	R-TA100-C2	85	ITVTYPE	Intervention Article Type	Positive Control
86	8325064	TX	SetR	R-TA100-C2	86	ITVCONC	Intervention Article Concentration	2
87	8325064	TX	SetR	R-TA100-C2	87	ITVCONCU	Intervention Article Concentration Unit	ug/plate
88	8325064	TX	SetR	R-TA100-C2	88	TRTV	Treatment Vehicle	DMSO

REFID values are defined by the applicant to uniquely identify the observational unit within an experimental unit. In the simplified diagram of an assay procedure (below), the test tube that contains the possible mutagen is an example of an entity that would have a REFID indicating information at the level of trial set. The petri plate created from that test tube and used to count revertant numbers is an example of an entity that would be at an observational level.

This picture does not depict the more complicated procedures, trial sets, or observational units for the example study. For study 8325064, the applicant chose to define the REFIDs at the trial set level with a single character (e.g., A, F, G, R) and chose to define REFIDs at the observational level based on the location of each tube in 1 of multiple exposure/incubation plates (e.g, 6_1 for plate 6, position 1).

Image Added

Dataset wrap

Name	relref

Rowcaps

Row 1:	Shows the value of REFID=A. This REFID refers to the trial set with a SETCD of "SetA", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET". TRIAL SET indicates this identifier relates to the entire trial set. EXPERIMENTAL UNIT indicates this identifier received the intervention article, DMSO.
Rows 2-6:	Show the values of 5 observational units (1_1 through 1_5) that are within the parent experimental unit, REFID=A.
Row 7:	Shows the value of REFID=F. This REFID refers to the trial set with a SETCD of "SetF", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET". TRIAL SET indicates this identifier relates to the entire trial set. EXPERIMENTAL UNIT indicates this identifier received the intervention article, TA1.
Rows 8-10:	Show the values of 3 observational units (6_1 through 6_3) that are within the parent experimental unit, REFID=F.
Row 11:	Shows the value of REFID=G. This REFID refers to the trial set with a SETCD of "SetG", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET". TRIAL SET indicates this identifier relates to the entire trial set. EXPERIMENTAL UNIT indicates this identifier received the intervention article, TA1.
Rows 12-14:	Show the values of 3 observational units (7_1 through 7_3) that are within the parent experimental unit, REFID=G.
Row 15:	Shows the value of REFID=R. This REFID refers to the trial set with a SETCD of "SetG", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET". TRIAL SET indicates this identifier relates to the entire trial set. EXPERIMENTAL UNIT indicates this identifier received the intervention article, NaN3.
Rows 16-18:	Show the values of 3 observational units (18_1 through 18_3) that are within the parent experimental unit, REFID=R.

Dataset2

tableid	relref.xpt

Row	STUDYID	SETCD	REFID	PARENT	LEVEL	LVLDESC
1	8325064	SetA	A		1	EXPERIMENTAL UNIT/TRIAL SET
2	8325064	SetA	1_1	A	2	OBSERVATIONAL UNIT
3	8325064	SetA	1_2	A	2	OBSERVATIONAL UNIT
4	8325064	SetA	1_3	A	2	OBSERVATIONAL UNIT
5	8325064	SetA	1_4	A	2	OBSERVATIONAL UNIT
6	8325064	SetA	1_5	A	2	OBSERVATIONAL UNIT
7	8325064	SetF	F		1	EXPERIMENTAL UNIT/TRIAL SET
8	8325064	SetF	6_1	F	2	OBSERVATIONAL UNIT
9	8325064	SetF	6_2	F	2	OBSERVATIONAL UNIT
10	8325064	SetF	6_3	F	2	OBSERVATIONAL UNIT
11	8325064	SetG	G		1	EXPERIMENTAL UNIT/TRIAL SET
12	8325064	SetG	7_1	G	2	OBSERVATIONAL UNIT
13	8325064	SetG	7_2	G	2	OBSERVATIONAL UNIT
14	8325064	SetG	7_3	G	2	OBSERVATIONAL UNIT
15	8325064	SetR	R		1	EXPERIMENTAL UNIT/TRIAL SET
16	8325064	SetR	18_1	R	2	OBSERVATIONAL UNIT
17	8325064	SetR	18_2	R	2	OBSERVATIONAL UNIT
18	8325064	SetR	18_3	R	2	OBSERVATIONAL UNIT

ou.xpt. Observational and Experimental Units domain

Experimental unit - The unit to which the treatment is applied, eg. Test tube

Observational unit - The unit on which the response is measured. (This may not be the same as the experimental unit.)

Dataset wrap

Name	gt

Rowcaps

Rows 1-5:

Show the number of revertant colonies per plate collected for each of 5 observational units, GTREFID=1_1 through 1_5 (see description in the RELREF dataset).

Rows 6, 7:

Show summary values collected (mean, standard deviation) for GTREFID=A that apply to the entire trial set, SetA, as indicated by LEVEL=1 and LVLDESC=TRIAL SET for this REFID as shown in the RELREF dataset.

Rows 8-13:

Revertent colonies were counted for each of 3 plates/observational units (GTREFID=6_1 through 6_3) and each value is associated with a record to show a postfix code of "V" (Very thin background bacterial lawn).

Rows 14-16:

Show summary values collected (mean, standard deviation, fold increase) for GTREFID=F that apply to the entire trial set, SetF, as indicated by LEVEL=1 and LVLDESC=TRIAL SET for this REFID in the RELREF dataset.

Rows 17-19:

Show 3 plates/observational units (GTREFID=7_1 through 7_3) where no revertant colonies were counted due to too much cytotoxicity and a postfix code of "T".

Jira

showSummary	false
server	Issue Tracker (JIRA)
columnIds	issuekey,summary,issuetype,created,updated,duedate,assignee,reporter,priority,status,resolution
columns	key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
serverId	85506ce4-3cb3-3d91-85ee-f633aaaf4a45
key	TOBA-668

Rows 20-22:

Show the number of revertant colonies per plate collected for each of 3 observational units (GTREFID=18_1 through 18_3).

Rows 23-25:

Show summary values collected (mean, standard deviation, fold increase) for GTREFID=R that apply to the entire trial set, SetR, as indicated by LEVEL=1 and LVLDESC=TRIAL SET for this REFID in the RELREF dataset.

Dataset2

Row	STUDYID	DOMAIN	GTSEQ	GTREFID	GTTESTCD	GTTEST	GTORRES	GTCOLSRT	GTSTRESC	GTSTRESN	GTSTAT	GTREASND	GTMETHOD	GTDTC
1	8325064	GT	1	1_1	RPP	Revertant Colony Numbers Per Plate	26		26	26			INSTRUMENT COUNTED	2015-08-03
2	8325064	GT	2	1_2	RPP	Revertant Colony Numbers Per Plate	35		35	35			INSTRUMENT COUNTED	2015-08-03
3	8325064	GT	3	1_3	RPP	Revertant Colony Numbers Per Plate	39		39	39			INSTRUMENT COUNTED	2015-08-03
4	8325064	GT	4	1_4	RPP	Revertant Colony Numbers Per Plate	35		35	35			INSTRUMENT COUNTED	2015-08-03
5	8325064	GT	5	1_5	RPP	Revertant Colony Numbers Per Plate	30		30	30			INSTRUMENT COUNTED	2015-08-03
6	8325064	GT	6	A	RPP	Revertant Colony Numbers Per Plate	33.0	MEAN	33.0	33.0				2015-08-03
7	8325064	GT	7	A	RPP	Revertant Colony Numbers Per Plate	5.0	STANDARD DEVIATION	5.0	5.0				2015-08-03
8	8325064	GT	8	6_1	RPP	Revertant Colony Numbers Per Plate	8		8	8			MANUALLY COUNTED	2015-08-03
9	8325064	GT	9	6_1	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn		V					2015-08-03
10	8325064	GT	10	6_2	RPP	Revertant Colony Numbers Per Plate	10		10	10			MANUALLY COUNTED	2015-08-03
11	8325064	GT	11	6_2	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn		V					2015-08-03
12	8325064	GT	12	6_3	RPP	Revertant Colony Numbers Per Plate	12		12	12			MANUALLY COUNTED	2015-08-03
13	8325064	GT	13	6_3	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn		V					2015-08-03
14	8325064	GT	14	F	RPPMEAN	Mean Rev Colony Num Per Plate	10.0	MEAN	10.0	10.0				2015-08-03
15	8325064	GT	15	F	RPPSTDDV	Std Dev Rev Colony Num Per Plate	2.0	STANDARD DEVIATION	2.0	2.0				2015-08-03
16	8325064	GT	16	F	RPPFLDIC	Fold Increase Rev Colony Num Per Plate	0.3	FOLD INCREASE	0.3	0.3				2015-08-03
17	8325064	GT	17	7_1	CYTOTOX	Cytotoxicity	Toxic No Revertant Colonies		T		NOT DONE	TOO MUCH CYTOTOXICITY		2015-08-03
18	8325064	GT	18	7_2	CYTOTOX	Cytotoxicity	Toxic No Revertant Colonies		T		NOT DONE	TOO MUCH CYTOTOXICITY		2015-08-03
19	8325064	GT	19	7_3	CYTOTOX	Cytotoxicity	Toxic No Revertant Colonies		T		NOT DONE	TOO MUCH CYTOTOXICITY		2015-08-03
20	8325064	GT	20	18_1	RPP	Revertant Colony Numbers Per Plate	812		812	812			INSTRUMENT COUNTED	2015-08-03
21	8325064	GT	21	18_2	RPP	Revertant Colony Numbers Per Plate	912		912	912			INSTRUMENT COUNTED	2015-08-03
22	8325064	GT	22	18_3	RPP	Revertant Colony Numbers Per Plate	839		839	839			INSTRUMENT COUNTED	2015-08-03
23	8325064	GT	23	R	RPPMEAN	Mean Rev Colony Num Per Plate	854.3	MEAN	854.3	854.3				2015-08-03
24	8325064	GT	24	R	RPPSTDDV	Std Dev Rev Colony Num Per Plate	51.7	STANDARD DEVIATION	51.7	51.7				2015-08-03
25	8325064	GT	25	R	RPPFLDIC	Fold Increase Rev Colony Num Per Plate	6.4	FOLD INCREASE	6.4	6.4				2015-08-03

Row 1:

Shows values collected for the set, SetA, as shown in the

Rows 2-4:

Show two records for Alkaline Phosphatase that were collected 1 day apart and are expected to be reported together. Row 4 shows how to create a derived record (average of the Rows 2 and 3) and flag it as Derived (LBDRVFL = "Y") as well as the record to use as baseline (LBBLFL = "Y").

Rows 6-7:

Show a suggested use of the LBSCAT variable. It could be used to further classify types of tests within a laboratory panel (e.g., "DIFFERENTIAL").

Row 9:

Shows the proper use of the LBSTAT variable to indicate "NOT DONE," when the fact that the test was done was documented.

Row 12:

The subject had Cholesterol measured. The normal range for this test is <200 mg/dL. The value <200 may not be used in the normal range variables LBORNRHI or LBSTNRHI; however, a sponsor may decide, e.g., to enter "0" into LBORNRLO and "199" in LBORNRHI. The sponsor must define the appropriate value for all of the normal range variables.

Row 13:

Shows the use of LBUSCHFL to indicate that the test result was obtained from an unscheduled blood collection. In this case, the subject was moribund and a blood sample was taken prior to sacrifice.

Rows 1, 6:

Use records in the SUPPLB dataset example to show biological significance assigned by the investigator for test results.

Dataset2

Row

STUDYID

ASSAYID

DOMAIN

SETCD (in TX)

EUID

OBUID

1

8325064

Ames

OU

SetA

VC1

2

123

MLA

OU

A1

4_-S9_C31.3_B

VC2

3

123

MLA

OU

A1

4_-S9_C31.3_B

VC3

4

123

MLA

OU

A1

4_-S9_C31.3_B

TFT1

5

123

MLA

OU

A1

4_-S9_C31.3_B

TFT2

6

123

MLA

OU

A1

4_-S9_C31.3_B

TFT3

7

123

MLA

OU

A2

4_-S9_C500_B

VC1

8

123

MLA

OU

A2

4_-S9_C500_B

VC2

9

123

MLA

OU

A2

4_-S9_C500_B

VC3

10

123

MLA

OU

A2

4_-S9_C500_B

TFT1

11

123

MLA

OU

A2

4_-S9_C500_B

TFT2

12

123

MLA

OU

A2

4_-S9_C500_B

TFT3

Expand

title	gt.xpt (similar to LB)

2015-08-032015-08-032015-08-032015-08-03

10.0

1037.3

31.4

Dataset wrap

Name	gt.xpt

Rowcaps

Rows 1-7:

Show values collected for the set, SetA.

Rows 8-15:

Shows values collected for the set, SetF.

Rows 6-7:

Show a suggested use of the LBSCAT variable. It could be used to further classify types of tests within a laboratory panel (e.g., "DIFFERENTIAL").

Rows 6,7,12,13, x,x,x,x:

Show values collected (e.g., MEAN, STANDARD DEVIATION, and/or FOLD INCREASE) that apply to all of the observational units within the experimental unit, as show by OBUID = "ALL".

Row 9:

Shows the proper use of the LBSTAT variable to indicate "NOT DONE," when the fact that the test was done was documented.

Row 12:

The subject had Cholesterol measured. The normal range for this test is <200 mg/dL. The value <200 may not be used in the normal range variables LBORNRHI or LBSTNRHI; however, a sponsor may decide, e.g., to enter "0" into LBORNRLO and "199" in LBORNRHI. The sponsor must define the appropriate value for all of the normal range variables.

Row 13:

Shows the use of LBUSCHFL to indicate that the test result was obtained from an unscheduled blood collection. In this case, the subject was moribund and a blood sample was taken prior to sacrifice.

Rows 1, 6:

Use records in the SUPPLB dataset example to show biological significance assigned by the investigator for test results.

Dataset2

Row

STUDYID

ASSAYID

DOMAIN

TXSETCD

EUID

OUID

GTSEQ

GTTESTCD

GTTEST

GTORRES

GTORRESU

GTCOLSRT (coll. summ. result type)

GTSTRESC

GTSTRESN

GTSTRESU

GTDTC

GTMETHOD

1

8325064

Ames

GT

SETA

A

0_1

1

RPP

Revertant Numbers Per Plate

26

COLONIES

26

COLONIES

INSTRUMENT COUNTED

2

8325064

Ames

GT

SETA

A

0_2

2

RPP

Revertant Numbers Per Plate

35

COLONIES

35

INSTRUMENT COUNTED

3

8325064

Ames

GT

SETA

A

0_3

3

RPP

Revertant Numbers Per Plate

39

COLONIES

39

INSTRUMENT COUNTED

4

8325064

Ames

GT

SETA

A

0_4

4

RPP

Revertant Numbers Per Plate

35

COLONIES

35

INSTRUMENT COUNTED

5

8325064

Ames

GT

SETA

A

0_5

5

RPP

Revertant Numbers Per Plate

30

COLONIES

30

2015-08-03

INSTRUMENT COUNTED

6

8325064

Ames

GT

SETA

A

ALL

6

RPP

Revertant Numbers Per Plate

33.0

COLONIES

MEAN

33.0

7

8325064

Ames

GT

SETA

A

ALL

7

RPP

Revertant Numbers Per Plate

5.0

COLONIES

STANDARD DEVIATION

5.0

INSTRUMENT COUNTED

8

8325064

Ames

GT

SETF

5_1

1

RPP

Revertant Numbers Per Plate

8

MANUALLY COUNTED

9

8325064

Ames

GT

SETF

5_1

1

10

8325064

Ames

GT

SETF

5_2

2

RPP

Revertant Numbers Per Plate

10

MANUALLY COUNTED

11

8325064

Ames

GT

SETF

5_3

3

RPP

Revertant Numbers Per Plate

12

MANUALLY COUNTED

12

8325064

Ames

GT

SETF

ALL

6

RPPMEAN

Mean of Revertant Numbers Per Plate

13

8325064

Ames

GT

SETF

ALL

7

RPPSTDDV

Standard Deviation of Revertant Numbers Per Plate

2.0

14

8325064

Ames

GT

SETF

ALL

8

RPPFDINC

Fold Increase of Revertant Numbers Per Plate

0.3

15

8325064

Ames

GT

SETF

9

CYTOTOX

Cytotoxicity

Very thin background bacterial lawn

V

8325064

Ames

GT

SETI

5_1

1

RPP

Revertant Numbers Per Plate

1104

8325064

Ames

GT

SETI

5_2

2

RPP

Revertant Numbers Per Plate

1037

8325064

Ames

GT

SETI

5_3

3

RPP

Revertant Numbers Per Plate

971

8325064

Ames

GT

SETI

ALL

6

RPPMEAN

Mean of Revertant Numbers Per Plate

8325064

Ames

GT

SETI

ALL

7

RPPSTDDV

Standard Deviation of Revertant Numbers Per Plate

66.5

8325064

Ames

GT

SETI

ALL

8

RPPFLDINC

Fold Increase of Revertant Numbers Per Plate

31.4

Page tree

Versions Compared

Old Version 23

New Version Current

Key