SEND Example.In vitro Bacterial Reverse Mutation Assay

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. The bacterial reverse mutation test uses four different amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and one strain of 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 S typhimurium and E. coli 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.

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
23	8325064	Ames	TS	1	3	SPECIES	Species	Escherichia coli
24	8325064	Ames	TS	1	3	STRAIN	Strain	WP2 uvrA pKM101

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Row captions have been provided, but there doesn't seem to be a dataset to which the row captions would apply.

How do we handle "toxic, no revertant colonies"? (LAK will add 6 records with GTSTAT = NOT DONE, GTREASND = "TOO MUCH CYTOTOXICITY,"
When "-" in Mean, Std Dev, Fold Inc - refer to SEND team's marked-up table (GTSTAT = NOT DONE; variety of REASND)

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 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.

Row Captions Debug Message

Remember to keep number agreement between labels and captions.

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	Ames	TX	SetA	A-TA98-C0	8	TRTDU	Treatment Duration Unit	HOURS
9	8325064	Ames	TX	SetA	A-TA98-C0	9	INCBTMP	Incubation Temperature	37
10	8325064	Ames	TX	SetA	A-TA98-C0	10	INCBTMPU	Incubation Temperature Unit	C
11	8325064	Ames	TX	SetA	A-TA98-C0	11	HUMID	Atmospheric Relative Humidity Percent	50
12	8325064	Ames	TX	SetA	A-TA98-C0	12	ATMCO2	Atmospheric CO2 Percent	5
13	8325064	Ames	TX	SetA	A-TA98-C0	13	SPTOBID	Sponsor defined tobacco identifier	CIG01a
14	8325064	Ames	TX	SetA	A-TA98-C0	14	EXPTYP	Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)	Submerged
15	8325064	Ames	TX	SetA	A-TA98-C0	15	SAMTYP	Sample Type	Total Particulate Matter in PBS
16	8325064	Ames	TX	SetA	A-TA98-C0	16	INTRVN	name of the intervention article	TA1
17	8325064	Ames	TX	SetA	A-TA98-C0	17	ITVTYPE	type of intervention article	Vehicle Control
18	8325064	Ames	TX	SetA	A-TA98-C0	18	ITVCONC	Concentration of intervention article	0
19	8325064	Ames	TX	SetA	A-TA98-C0	19	ITVCONCU	Concentration Unit	ug/plate
20	8325064	Ames	TX	SetA	A-TA98-C0	20	TRTV	Treatment Vehicle	DMSO
21	8325064	Ames	TX	SetA	A-TA98-C0	21	SPDEVID	Sponsor defined device identifier	PUFFMASTER3K
22	8325064	Ames	TX	SetA	A-TA98-C0	22	DUREFID	Smoke Regimen	Medium Intensity Regimen
23	8325064	Ames	TX	SetF	F-TA98-C500	1	SPECIES	Species
24	8325064	Ames	TX	SetF	F-TA98-C500	2	STRAIN	Strain/Substrain
25	8325064	Ames	TX	SetF	F-TA98-C500	3	METACT	Metabolic Activation
26	8325064	Ames	TX	SetF	F-TA98-C500	4	METACTFL	Y/N presence of metabolic activation	N
27	8325064	Ames	TX	SetF	F-TA98-C500		TRTDRTOL	Treatment Duration Tolerance
28	8325064	Ames	TX	SetF	F-TA98-C500		TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetF	F-TA98-C500		INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	TA1
	8325064	Ames	TX	SetF	F-TA98-C500		ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Product
	8325064	Ames	TX	SetF	F-TA98-C500		ITVCONC	Concentration of intervention article	500
	8325064	Ames	TX	SetF	F-TA98-C500		ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetF	F-TA98-C500		STRAIN	Strain/Substrain	TA98
	8325064	Ames	TX	SetF	F-TA98-C500		REGIME	Smoking Regime	ISO Regime
...













	8325064	Ames	TX	SetG (row 7) do G not I!!!			METACT	Metabolic Activation (should there be two parms? Presence, type)?	None
	8325064	Ames	TX	SetG			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	SetG			TRTDRTOL	Treatment Duration Tolerance
	8325064	Ames	TX	SetG			TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
	8325064	Ames	TX	SetG			INTRVN	name of the intervention article (Tobacco ProdA, Bleomycin or Cyclophosphamid A)	2-Nitrofluorine
	8325064	Ames	TX	SetG			ITVTYPE	type of intervention article choices of values: product; negative control; positive control	Positive Control
	8325064	Ames	TX	SetG			ITVCONC	Concentration of intervention article	5
	8325064	Ames	TX	SetG			ITVCONCU	Concentration Unit	ug/plate
	8325064	Ames	TX	SetG			REGIME	Smoking Regime	ISO
...				SetG
	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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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.

Row Captions Debug Messages

Remember to keep number agreement between labels and captions.
Please construct row caption labels as instructed in <ac:link><ri:page ri:content-title="Constructing labels for row captions" ri:space-key="TTD"/></ac:link>.

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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	26	COLONIES	2015-08-03	INSTRUMENT COUNTED
2	8325064	Ames	GT	SETA	A	0_2	2	RPP	Revertant Numbers Per Plate	35	COLONIES		35	35		2015-08-03	INSTRUMENT COUNTED
3	8325064	Ames	GT	SETA	A	0_3	3	RPP	Revertant Numbers Per Plate	39	COLONIES		39	39		2015-08-03	INSTRUMENT COUNTED
4	8325064	Ames	GT	SETA	A	0_4	4	RPP	Revertant Numbers Per Plate	35	COLONIES		35	35		2015-08-03	INSTRUMENT COUNTED
5	8325064	Ames	GT	SETA	A	0_5	5	RPP	Revertant Numbers Per Plate	30	COLONIES		30	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	33.0
7	8325064	Ames	GT	SETA	A	ALL	7	RPP	Revertant Numbers Per Plate	5.0	COLONIES	STANDARD DEVIATION	5.0	5.0
8	8325064	Ames	GT	SETF	F	6_1	1	RPP	Revertant Numbers Per Plate	8	COLONIES		8	8			MANUALLY COUNTED
9	8325064	Ames	GT	SETF	F	6_1	2	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn	COLONIES		V
10	8325064	Ames	GT	SETF	F	6_2	3	RPP	Revertant Numbers Per Plate	10	COLONIES		10	10			MANUALLY COUNTED
11	8325064	Ames	GT	SETF	F	6_3	4	RPP	Revertant Numbers Per Plate	12	COLONIES		12	12			MANUALLY COUNTED
12	8325064	Ames	GT	SETF	F	ALL	5	RPPMEAN	Mean of Revertant Numbers Per Plate	10.0	COLONIES	MEAN	10.0	10.0
13	8325064	Ames	GT	SETF	F	ALL	6	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	2.0	COLONIES	STANDARD DEVIATION	2.0	2.0
14	8325064	Ames	GT	SETF	F	ALL	7	RPPFDINC	Fold Increase of Revertant Numbers Per Plate	0.3	COLONIES	FOLD INCREASE	0.3	0.3
	8325064	Ames	GT	SETG	G	5_1	1	RPP	Revertant Numbers Per Plate	1104			1104	1104
	8325064	Ames	GT	SETG	G	5_2	2	RPP	Revertant Numbers Per Plate	1037			1037	1037
	8325064	Ames	GT	SETG	G	5_3	3	RPP	Revertant Numbers Per Plate	971			971	971
	8325064	Ames	GT	SETR	R	ALL		RPPMEAN	Mean of Revertant Numbers Per Plate	1037.3			1037.3	1037.3
	8325064	Ames	GT	SETR	R	ALL		RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	66.5			66.5	66.5
	8325064	Ames	GT	SETR	R	ALL		RPPFLDINC	Fold Increase of Revertant Numbers Per Plate	31.4			31.4	31.4

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SEND Example.In vitro Bacterial Reverse Mutation Assay