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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 trial design and results from the in vitro bacterial reverse mutation test of Study #8325064.

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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	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	8325064	Ames	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	8325064	Ames	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	8325064	Ames	TS	1		STSTDTC	Study Start Date	2015-07-29
4	8325064	Ames	TS	1		STITLE	Study Title	The Bacterial Reverse Mutation Test, Study 8325064-1
5	8325064	Ames	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	8325064	Ames	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	8325064	Ames	TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8	8325064	Ames	TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9	8325064	Ames	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
10	8325064	Ames	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	8325064	Ames	TS	1	1	TFCNTRY	Test Facility Country	USA
12	8325064	Ames	TS	1	1	STDIR	Study Director	Dr. R. Smith
13	8325064	Ames	TS	1		GLPFL	GLP Flag	N
14	8325064	Ames	TS	1		ASTD	Assay Standard	OECD Test No. 471
15	8325064	Ames	TS	1		ASTDV	Assay Standard Version	2020-06-29
16	8325064	Ames	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
17	8325064	Ames	TS	1		SSSTYP	Study Sub Type	Bacterial Reverse Mutation Test
18	8325064	Ames	TS	1	2	SPECIES	Species	Salmonella
19	8325064	Ames	TS	1	2	STRAIN	Strain	TA98
20	8325064	Ames	TS	1	2	STRAIN	Strain	TA100
21	8325064	Ames	TS	1	2	STRAIN	Strain	TA1535
22	8325064	Ames	TS	1	2	STRAIN	Strain	TA1537
1823	8325064	Ames	TS	1	3	SPECIES	Species	Escherichia coli
1924	8325064	Ames	TS	1	3	STRAIN	Strain	WP2 uvrA pKM101	20	8325064	Ames	TS	1	CELLLN	Cell Line (this would be Tester Strain for Ames)	TA98

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title	tx.xpt (trial sets)

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)

Below the SETS shown in the TX table are rows A, F, I, and R (probably don't need R)

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET (what sponsor calls it)	TXPARMCD	TXPARM	TXVAL
1	8325064	Ames	TX	SetA	A-TA98-C0	SPECIES	Species	Salmonella typhimurium
92	8325064	Ames	TX	SetA	A-TA98-C0	STRAIN	Strain/Substrain	TA98
13	8325064	Ames	TX	SetA (Row 1)	A-TA98-C0	METACT	Metabolic Activation
4						METACTFL	Y/N presence of metabolic activation	N
25	8325064	Ames	TX	SetA		TRTDMIN	Treatment Duration Minimum	71.5
36	8325064	Ames	TX	SetA		TRTDTRG	Treatment Duration Target	72
47	8325064	Ames	TX	SetA		TRTDMAX	Treatment Duration Maximum	72.5
8	8325064	Ames	TX	SetA		TRTDU	Treatment Duration Unit	HOURS
9	8325064	Ames	TX	SetA		INCBTMP	Incubation Temperature	37
10	8325064	Ames	TX	SetA		INCBTMPU	Incubation Temperature Unit	C
11	8325064	Ames	TX	SetA		HUMID	Atmospheric Relative Humidity Percent	50
12	8325064	Ames	TX	SetA		ATMCO2	Atmospheric CO2 Percent	5
13	8325064	Ames	TX	SetA		SPTOBID	Sponsor defined tobacco identifier	CIG01a
14	8325064	Ames	TX	SetA		EXPTYP	Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)	Submerged
15	8325064	Ames	TX	SetA		SAMTYP	Sample Type	Total Particulate Matter in PBS
516	8325064	Ames	TX	SetA		INTRVN	name of the intervention article	DMSOTA1
617	8325064	Ames	TX	SetA		ITVTYPE	type of intervention article	Vehicle Control
718	8325064	Ames	TX	SetA		ITVCONC	Concentration of intervention article	0
819	8325064	Ames	TX	SetA		ITVCONCU	Concentration Unit	ug/plate
20	8325064	Ames	TX	SetA		TRTV	Treatment Vehicle	DMSO
21	8325064	Ames	TX	SetA		SPDEVID	Sponsor defined device identifier	PUFFMASTER3K
...						DUREFID	Smoke Regimen	Medium Intensity Regimen
	8325064	Ames	TX	SetF (row 6)		METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetF		TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
	8325064	Ames	TX	SetF		TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetF		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetF		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	TA1
	8325064	Ames	TX	SetF		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Product
	8325064	Ames	TX	SetF		ITVCONC	Concentration of intervention article	500
	8325064	Ames	TX	SetF		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetF		STRAIN	Strain/Substrain	TA98
	8325064	Ames	TX	SetF		REGIME	Smoking Regime	ISO Regime
...
	8325064	Ames	TX	SetI(row 9)		METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetI		TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
	8325064	Ames	TX	SetI		TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetI		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetI		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	2-Nitrofluorine
	8325064	Ames	TX	SetI		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Positive Control
	8325064	Ames	TX	SetI		ITVCONC	Concentration of intervention article	5
	8325064	Ames	TX	SetI		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetI		REGIME	Smoking Regime	ISO
...
	8325064	Ames	TX	SetR (Row 18)		METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetR		TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
	8325064	Ames	TX	SetR		TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetR		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetR		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	4-Nitroquinoline-1-oxide
	8325064	Ames	TX	SetR		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Positive Control
	8325064	Ames	TX	SetR		ITVCONC	Concentration of intervention article	2
	8325064	Ames	TX	SetR		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetR		STRAIN	Strain/Substrain	TA98
	8325064	Ames	TX	SetR		REGIME	Smoking Regime	ISO

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Key

SET (what sponsor calls it)