You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 46 Next »

  1. move assumptions out of all of the examples

  2. 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.

In this example, the Trial Summary dataset, ts.xpt, includes many informational fields that may provide context at the study level, for Study 8325064.  Also, TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1) and records related to the Test Site (TSGRPID = 2). The Study Director is associated with the Test Facility and the Principal Investigator is associated with the Test Site. Finally, the Primary Treatment CAS Registry Number is not known and this is recorded as an empty TSVAL and UNKNOWN in the corresponding TSVALNF.

Rows 1-2:Show two records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP Types apply for this example study.
Rows 9-12: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 18-24:Show that this example study includes two different species of bacteria and a total of five strains.
Rows 18-22:Show that TSGRPID (TSGRPID = 2) has been used to link the information for one species (Salmonella) with four different strains that are tested in this example study.
Rows 23-24:Show that TSGRPID (TSGRPID = 3) has been used to link the information for one species (Escherichia coli) with the strain that is tested in this example study.

ts.xpt

xx.xpt

Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1

8325064AmesTS1
GLPTYPGood Laboratory Practice TypeFDA

2

8325064AmesTS2
GLPTYPGood Laboratory Practice TypeOECD

3

8325064AmesTS1
STSTDTCStudy Start Date2015-07-29

4

8325064AmesTS1
STITLEStudy Title

The Bacterial Reverse Mutation Test, Study 8325064-1


5

8325064AmesTS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0

6

8325064AmesTS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30

7

8325064AmesTS1
SSPONSORSponsor OrganizationExample Sponsor Inc.

8

8325064AmesTS1
SPREFIDSponsor's Study Reference ID
NOT APPLICABLE

9

8325064AmesTS11TSTFNAMTest Facility NameExample Tox Lab Name

10

8325064AmesTS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000

11

8325064AmesTS11TFCNTRYTest Facility CountryUSA

12

8325064AmesTS11STDIRStudy DirectorDr. R. Smith

13

8325064AmesTS1
GLPFLGLP FlagN

14

8325064AmesTS1
ASTDAssay StandardOECD Test No. 471

15

8325064AmesTS1
ASTDVAssay Standard Version2020-06-29

16

8325064AmesTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO

17

8325064AmesTS1
SSSTYPStudy Sub TypeBacterial Reverse Mutation Test

18

8325064AmesTS12SPECIESSpeciesSalmonella

19

8325064AmesTS12STRAINStrainTA98

20

8325064AmesTS12STRAINStrainTA100

21

8325064AmesTS12STRAINStrainTA1535

22

8325064AmesTS12STRAINStrainTA1537

23

8325064AmesTS13SPECIESSpeciesEscherichia coli

24

8325064AmesTS13STRAINStrainWP2 uvrA pKM101
$warningHtml

Dataset Wrapper Debug Message

Please add a row column to your dataset.

This example trial set dataset shows information about the test conditions for SetA and SetR in this example study. For brevity, this does not show information for SetF, SetG, or any other sets.  A fully formed tx.xpt for this example study would include information about the test conditions for all sets. 

Rows 1-22:Show trial set parameters and trial set values that comprise the test conditions for the set SetA. SetA is the data for 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 table Raw Data for Study 8325064.
Rows 23-44:Show trial set parameters and trial set values that comprise the test conditions for the set SetR. SetR is the data for the vehicle control (i.e., Strain of TA100, positive control with a concentration value of 2). SetR is associated with the eighteenth row, labeled "SetR", in the table Raw Data for Study 8325064.
$titleHtml

tx.xpt trial sets.xpt

RowSTUDYIDASSAYIDDOMAINSETCDSETTXSEQTXPARMCDTXPARMTXVAL
18325064AmesTX

SetA

A-TA98-C01SPECIESSpeciesSalmonella typhimurium
28325064AmesTXSetAA-TA98-C02STRAINStrain/SubstrainTA98
38325064AmesTX

SetA 

A-TA98-C03METACTMetabolic Activation  
48325064AmesTX

SetA 

A-TA98-C04METACTFLY/N presence of metabolic activationN
58325064AmesTXSetAA-TA98-C05TRTDMINTreatment Duration Minimum71.5
68325064AmesTXSetAA-TA98-C06TRTDTRGTreatment Duration Target72
78325064AmesTXSetAA-TA98-C07TRTDMAXTreatment Duration Maximum72.5
88325064AmesTXSetAA-TA98-C08TRTDUTreatment Duration UnitHOURS
98325064AmesTXSetAA-TA98-C09INCBTMPIncubation Temperature37
108325064AmesTXSetAA-TA98-C010INCBTMPUIncubation Temperature UnitC
118325064AmesTXSetAA-TA98-C011HUMIDAtmospheric Relative Humidity  Percent50
128325064AmesTXSetAA-TA98-C012ATMCO2Atmospheric CO2 Percent5
138325064AmesTXSetAA-TA98-C013SPTOBID

Sponsor defined tobacco identifier

CIG01a
148325064AmesTXSetAA-TA98-C014EXPTYP

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

Submerged
158325064AmesTXSetAA-TA98-C015SAMTYP 

Sample Type

Total Particulate Matter in PBS
168325064AmesTXSetAA-TA98-C016INTRVN

name of the intervention article

TA1
178325064AmesTXSetAA-TA98-C017ITVTYPE

type of intervention article

Vehicle Control
188325064AmesTXSetAA-TA98-C018ITVCONCConcentration of intervention article0
198325064AmesTXSetAA-TA98-C019ITVCONCUConcentration Unitug/plate
208325064AmesTXSetAA-TA98-C020TRTVTreatment VehicleDMSO
218325064AmesTXSetAA-TA98-C021SPDEVIDSponsor defined device identifierPUFFMASTER3K
228325064AmesTXSetAA-TA98-C022DUREFIDSmoke RegimenMedium Intensity Regimen
238325064AmesTX

SetR

R-TA100-C21SPECIESSpeciesSalmonella typhimurium
248325064AmesTX

SetR

R-TA100-C22STRAINStrain/SubstrainTA100
258325064AmesTX

SetR

R-TA100-C23METACTMetabolic Activation  
268325064AmesTX

SetR

R-TA100-C24METACTFLY/N presence of metabolic activationN
278325064AmesTX

SetR

R-TA100-C25TRTDMINTreatment Duration Minimum71.5
288325064AmesTX

SetR

R-TA100-C26TRTDTRGTreatment Duration Target72
298325064AmesTX

SetR

R-TA100-C27TRTDMAXTreatment Duration Maximum72.5
308325064AmesTX

SetR

R-TA100-C28TRTDUTreatment Duration UnitHOURS
318325064AmesTX

SetR

R-TA100-C29INCBTMPIncubation Temperature37
328325064AmesTX

SetR

R-TA100-C210INCBTMPUIncubation Temperature UnitC
338325064AmesTX

SetR

R-TA100-C211HUMIDAtmospheric Relative Humidity  Percent50
348325064AmesTX

SetR

R-TA100-C212ATMCO2Atmospheric CO2 Percent5
358325064AmesTX

SetR

R-TA100-C213SPTOBID

Sponsor defined tobacco identifier

CIG01a
368325064AmesTX

SetR

R-TA100-C214EXPTYP

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

Submerged
378325064AmesTX

SetR

R-TA100-C215SAMTYP 

Sample Type

Total Particulate Matter in PBS
388325064AmesTX

SetR

R-TA100-C216INTRVN

name of the intervention article

TA1
398325064AmesTX

SetR

R-TA100-C217ITVTYPE

type of intervention article

Positive Control
408325064AmesTX

SetR

R-TA100-C218ITVCONCConcentration of intervention article2
418325064AmesTX

SetR

R-TA100-C219ITVCONCUConcentration Unitug/plate
428325064AmesTX

SetR

R-TA100-C220TRTVTreatment VehicleDMSO
438325064AmesTX

SetR

R-TA100-C221SPDEVIDSponsor defined device identifierPUFFMASTER3K
448325064AmesTX

SetR

R-TA100-C222DUREFIDSmoke RegimenMedium Intensity Regimen
45








46








47








48









8325064AmesTX


METACTMetabolic Activation  (should there be two parms? Presence, type)?None

8325064AmesTX


TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)

8325064AmesTX


TRTDRTOLTreatment Duration Tolerance

8325064AmesTX


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

8325064AmesTX


INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

2-Nitrofluorine

8325064AmesTX


ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Positive Control

8325064AmesTX


ITVCONCConcentration of intervention article5

8325064AmesTX


ITVCONCUConcentration Unitug/plate

8325064AmesTX


REGIMESmoking RegimeISO
...









8325064AmesTX


METACTMetabolic Activation  (should there be two parms? Presence, type)?None

8325064AmesTX


TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)

8325064AmesTX


TRTDRTOLTreatment Duration Tolerance

8325064AmesTX


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

8325064AmesTX


INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

4-Nitroquinoline-1-oxide

8325064AmesTX


ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Positive Control

8325064AmesTX


ITVCONCConcentration of intervention article2

8325064AmesTX


ITVCONCUConcentration Unitug/plate

8325064AmesTXSetR

STRAINStrain/SubstrainTA98

8325064AmesTXSetR

REGIMESmoking RegimeISO
$warningHtml

Dataset Wrapper Debug Message

Please add a row column to your dataset.

Observational Unit Identifiers (OBUIDs) are defined by the sponsor to uniquely identify the observational unit within an experimental unit. In this example the sponsor chose to define the EUIDs based on trial sets (e.g., F) and OBUIDs based on the position of the tube in one of multiple exposure/incubation plates (e.g, 6_1 for plate 6, position 1).


Rows 1-5:Show the values for OBUID within the experimental unit identifier, A, for Set A, as defined in the trial set dataset.
Rows 6-8:Show the values for OBUID within the experimental unit identifier, F, for Set F, as defined in the trial set dataset.
Rows 9-11:Show the values for OBUID within the experimental unit identifier, G, for Set G, as defined in the trial set dataset.
Rows 12-14:Show the values for OBUID within the experimental unit identifier, R, for Set R, as defined in the trial set dataset.
$titleHtml

ou.xpt observational and experimentat unit identifiers.xpt

RowSTUDYIDASSAYIDDOMAINSETCD EUID OBUID  
18325064AmesOUSetAA0_1
28325064AmesOUSetAA0_2
38325064AmesOUSetAA0_3
48325064AmesOUSetAA0_4
58325064AmesOUSetAA0_5

6

8325064AmesOUSetFF6_1
78325064AmesOUSetFF6_2
88325064AmesOUSetFF6_3
98325064AmesOUSetGG7_1
108325064AmesOUSetGG7_2
118325064AmesOUSetG

G

7_3
128325064AmesOUSetRR18_1
138325064AmesOUSetRR18_2
148325064AmesOUSetRR18_3
$warningHtml

Dataset Wrapper Debug Message

Please add a row column to your dataset.

Rows 1-7:Show values collected for the set, SetA.
Rows 8-16:Shows values collected for the set, SetF. Revertent colonies were counted and each value is associated with a record to show a postfix of code of "V".
Rows 17-19:Shows values collected for the set, SetG. Each record for this EUID shows the postfix code of "T". No revertent colonies were counted and there are no summary values collected.
Rows 20-25:Shows values collected for the set, SetR.
Rows 6,7,14,15,16, 23,24,25:Show summary values collected (e.g., MEAN, STANDARD DEVIATION, and/or FOLD INCREASE) that apply to all of the observational units within the experimental unit, as shown by OBUID = "ALL".

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>.

gt.xpt

gt.xpt.xpt

RowSTUDYIDASSAYIDDOMAINTXSETCDEUIDOUIDGTSEQGTTESTCDGTTESTGTORRESGTORRESUGTCOLSRT (coll. summ. result type)GTSTRESCGTSTRESNGTSTRESUGTSTATGTREASNDGTMETHODGTDTC
18325064AmesGTSETA A0_11RPPRevertant Numbers Per Plate26COLONIES
2626COLONIES

INSTRUMENT COUNTED


2015-08-03
28325064AmesGTSETA A0_22RPPRevertant Numbers Per Plate35COLONIES
3535COLONIES

INSTRUMENT COUNTED
2015-08-03
38325064AmesGTSETA A0_33RPPRevertant Numbers Per Plate39COLONIES
3939COLONIES

INSTRUMENT COUNTED
2015-08-03
48325064AmesGTSETA A0_44RPPRevertant Numbers Per Plate35COLONIES
3535COLONIES

INSTRUMENT COUNTED


2015-08-03
58325064AmesGTSETA A0_55RPPRevertant Numbers Per Plate30COLONIES
3030COLONIES

INSTRUMENT COUNTED2015-08-03
68325064AmesGTSETA AALL6RPPRevertant Numbers Per Plate33.0COLONIESMEAN33.033.0COLONIES



2015-08-03
78325064AmesGTSETA AALL7RPPRevertant Numbers Per Plate5.0COLONIESSTANDARD DEVIATION5.05.0COLONIES



2015-08-03
88325064AmesGTSETFF6_11RPPRevertant Numbers Per Plate8COLONIES
88COLONIES

MANUALLY COUNTED
2015-08-03
98325064AmesGTSETFF6_12CYTOTOXCytotoxicityVery thin background bacterial lawn

V





2015-08-03
108325064AmesGTSETF F6_23RPPRevertant Numbers Per Plate10COLONIES
1010COLONIES

MANUALLY COUNTED2015-08-03
118325064AmesGTSETFF6_22CYTOTOXCytotoxicityVery thin background bacterial lawn

V





2015-08-03
128325064AmesGTSETF F6_34RPPRevertant Numbers Per Plate12COLONIES
1212COLONIES

MANUALLY COUNTED
2015-08-03
138325064AmesGTSETFF6_32CYTOTOXCytotoxicityVery thin background bacterial lawn

V





2015-08-03
148325064AmesGTSETFFALL5RPPMEANMean of Revertant Numbers Per Plate

10.0


COLONIESMEAN

10.0


10.0


COLONIES



2015-08-03
158325064AmesGTSETF FALL6RPPSTDDVStandard Deviation of Revertant Numbers Per Plate2.0COLONIESSTANDARD DEVIATION2.02.0COLONIES


2015-08-03
168325064AmesGTSETF FALL7RPPFDINCFold Increase of Revertant Numbers Per Plate0.3COLONIESFOLD INCREASE0.30.3COLONIES



2015-08-03
178325064AmesGTSETGG5_11CYTOTOXCytotoxicityToxic No Revertant 
Colonies


T

NOT DONETOO MUCH CYTOTOXICITY

2015-08-03
188325064AmesGTSETGG5_22CYTOTOXCytotoxicityToxic No Revertant 
Colonies


T

NOT DONETOO MUCH CYTOTOXICITY

2015-08-03
198325064AmesGTSETGG5_33CYTOTOXCytotoxicityToxic No Revertant 
Colonies


T

NOT DONETOO MUCH CYTOTOXICITY

2015-08-03
208325064AmesGTSETRR18_11RPPRevertant Numbers Per Plate

812

COLONIES


812

812

COLONIES

INSTRUMENT COUNTED

2015-08-03
218325064AmesGTSETRR18_22RPPRevertant Numbers Per Plate

912

COLONIES


912

912

COLONIES

INSTRUMENT COUNTED
2015-08-03
228325064AmesGTSETRR18_33RPPRevertant Numbers Per Plate

839

COLONIES


839

839

COLONIES

INSTRUMENT COUNTED
2015-08-03
238325064AmesGTSETRRALL4RPPMEANMean of Revertant Numbers Per Plate854.3COLONIESMEAN854.3854.3COLONIES



2015-08-03
248325064AmesGTSETRRALL5RPPSTDDVStandard Deviation of Revertant Numbers Per Plate51.7COLONIESSTANDARD DEVIATION51.751.7COLONIES



2015-08-03
258325064AmesGTSETRRALL6RPPFLDINCFold Increase of Revertant Numbers Per Plate6.4COLONIESFOLD INCREASE6.46.4COLONIES


2015-08-03

Dataset Debug Messages

  • There are 14 leading, trailing, or non-breaking spaces in the dataset.
  • Please remove all formatting (see How to Clear Formatting).
  • Please remove all paragraph and/or line breaks.

Dataset Wrapper Debug Message

Please add a row column to your dataset.

  • No labels