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save genetic tox (AMES) word doc in working files (see email from Bill today)
populate units of COLONIES
recreate the data table - clean up, add "S" to the first set A

This is an example showing trial design and results from the in vitro bacterial reverse mutation test of Study #8325064.

The bacterial reverse mutation test uses amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and Escherichia coli (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.

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

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		SPECIES	Species	Salmonella
19	8325064	Ames				STRAIN	Strain	Salmonella typhimurium,
20	8325064	Ames	TS	1		CELLLN	Cell Line (this would be Tester Strain for Ames)	TA98 (examples: H292, CHO, TK6.. etc.)

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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)
What do we do for defined regimes (e.g. ISO Regime, Canadian ..) or all attributes should be listed as expected variables to allow for all including custom regimes (Puff volume, etc.)

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

Row	STUDYID	ASSAYID	DOMAIN	SETCD	TXPARMCD	TXPARM	TXVAL
1	8325064	Ames	TX	SetA (Row 1)	METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
2	8325064	Ames	TX	SetA	TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)
3	8325064	Ames	TX	SetA	TRTDRTOL	Treatment Duration Tolerance
4	8325064	Ames	TX	SetA	TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
5	8325064	Ames	TX	SetA	INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	DMSO
6	8325064	Ames	TX	SetA	ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Vehicle Control
7	8325064	Ames	TX	SetA	ITVCONC	Concentration of intervention article	0 (because no TA is used, this is just DMSO)
8	8325064	Ames	TX	SetA	ITVCONCU	Concentration Unit	ug/plate
9	8325064	Ames	TX	SetA	STRAIN	Strain/Substrain	TA98
10	8325064	Ames	TX	SetA	REGIME	Smoking Regime	ISO Regime
...
	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	STRAIN	Strain/Substrain	TA98
	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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title	gt.xpt (similar to LB)

Row	STUDYID	ASSAYID	DOMAIN	TXSETCD	EUID

PLTWLID

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	26	COLONIES	2015-08-03	INSTRUMENT COUNTED
2	8325064	Ames	GT	SETA	A	0_2	2	RPP	Revertant Numbers Per Plate	35		35	35		2015-08-03	INSTRUMENT COUNTED
3	8325064	Ames	GT	SETA	A	0_3	3	RPP	Revertant Numbers Per Plate	39		39	39		2015-08-03	INSTRUMENT COUNTED
4	8325064	Ames	GT	SETA	A	0_4	4	RPP	Revertant Numbers Per Plate	35		35	35		2015-08-03	INSTRUMENT COUNTED
5	8325064	Ames	GT	SETA	A	0_5	5	RPP	Revertant Numbers Per Plate	30		30	30		2015-08-03	INSTRUMENT COUNTED
6	8325064	Ames	GT	SETA	A	ALL	6	RPPMEAN	Mean of Revertant Numbers Per Plate	33.0		33.0	33.0			INSTRUMENT COUNTED
	8325064	Ames	GT	SETA				RPP	Revertant Numbers Per Plate
7	8325064	Ames	GT	SETA		ALL	7	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	5.0		5.0	5.0			INSTRUMENT COUNTED
	8325064	Ames	GT	SETF		5_1	1	RPP	Revertant Numbers Per Plate	8		8	8			MANUALLY COUNTED
	8325064	Ames	GT	SETF		5_1	1
	8325064	Ames	GT	SETF		5_2	2	RPP	Revertant Numbers Per Plate	10		10	10			MANUALLY COUNTED

	8325064	Ames	GT	SETF		5_3	3	RPP	Revertant Numbers Per Plate	12		12	12			MANUALLY COUNTED
	8325064	Ames	GT	SETF		ALL	6	RPPMEAN	Mean of Revertant Numbers Per Plate	10.0		10.0	10.0
	8325064	Ames	GT	SETF		ALL	7	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	2.0		2.0	2.0
	8325064	Ames	GT	SETF		ALL	8	RPPFLDINC	Fold Increase of Revertant Numbers Per Plate	0.3		0.3	0.3
	8325064	Ames	GT	SETI		5_1	1	RPP	Revertant Numbers Per Plate	1104		1104	1104
	8325064	Ames	GT	SETI		5_2	2	RPP	Revertant Numbers Per Plate	1037		1037	1037
	8325064	Ames	GT	SETI		5_3	3	RPP	Revertant Numbers Per Plate	971		971	971
	8325064	Ames	GT	SETI		ALL	6	RPPMEAN	Mean of Revertant Numbers Per Plate	1037.3		1037.3	1037.3
	8325064	Ames	GT	SETI		ALL	7	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	66.5		66.5	66.5
	8325064	Ames	GT	SETI		ALL	8	RPPFLDINC	Fold Increase of Revertant Numbers Per Plate	31.4		31.4	31.4

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Old Version 14

New Version 15

Key

SET (what sponsor calls it)