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Rowcaps |
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Rows 1-2: | Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this example 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). | | Shows the study type for this study. | | Shows that this study includes a Neutral Red Uptake Assay. | Rows 19-20: | Show that the species is human and the cell line is NHK in this study. |
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title | ts.xpt (trial summary, study level parameters) |
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- Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data.
- Assumption: A Trial (study) can have more than one assay type
- Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study
- Sponsor should be "applicant", how do we represent this? In text explanation in the IG? In definition in CT/Parmcd/Parm? ** Need to have CT discussion, include Erin M.**
- TK6, human keratinocyte, is this the "test system"?
- Can we draft a starting list of Study Types and Sub Types to submit to CT now?
- Is there a dictionary of species and/or strain that we would use? (see example)
| Row | STUDYID | ASSAYID | DOMAIN | TSSEQ | TSGRPID | TSPARMCD | TSPARM | TSVAL | TSVALNF |
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1 | 123 |
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NRU | TS | 1 |
| GLPTYP | Good Laboratory Practice Type | FDA |
| 2 | 123 |
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NRU | TS | 2 |
| GLPTYP | Good Laboratory Practice Type | OECD |
| 3 | 123 |
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NRU | TS | 1 |
| STSTDTC | Study Start Date | 2022-05-25 |
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4NRU | TS | 1 |
| STITLE | Study Title | Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay |
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5NRU | TS | 1 |
| SNDIGVER | SEND Implementation Guide Version | TOBACCO IMPLEMENTATION GUIDE VERSION 1.0 |
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6NRU | TS | 1 |
| SNDCTVER | SEND Controlled Terminology Version | SEND Terminology 2021-09-30 |
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7NRU | SSPONSORSponsor 's Organization8NRU | SPREFIDSponsor's 's Study Reference ID |
| NOT APPLICABLE |
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9NRU | TS | 1 | 1 | TSTFNAM | Test Facility Name | Example |
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Tox Testing 10NRU | TS | 1 | 1 | TSTFLOC | Test Facility Location | 10 Somewhere Street, Montgomery, AL 10000 |
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11NRU | TS | 1 | 1 | TFCNTRY | Test Facility Country | USA |
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12NRU | TS | 1 | 1 | STDIR | Study Director | Dr. R. Smith |
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13NRUGLPFLGLP Flag | Y | 14 | 123 | NRU | TS | 1 | ASTD | Assay Standard | NIH TSTGDNAM | Testing Guideline Name |
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Publication No. 07-4519 |
| 15 | 123 |
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NRUASTDV | 4 | TSTGDORG | Testing Guideline Organization | NIH |
| 16 | 123 | TS | 1 | 4 | TSTGDVER | Testing Guideline |
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Assay Standard 16NRU | TS | 1 |
| SSTYP | Study Type | GENOTOXICITY IN VITRO |
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17NRU | SSSTYP | Study Sub Type | In Vitro Neutral Red Uptake |
| GNTXAID | Genetic Toxicology Assay Identifier | NRU |
| 19 | 123 |
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18 | 123 | NRUSalmonella enterica 19NRU | ?? | Test System?? | TK6 Normal Human Keratinocyte |
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- Assumption: The Trial Sets (TX) domain provides the list of distinct sets of subjects having different experimental factors, treatment factors, inherent characteristics, or distinct
sponsor applicant designations as specified in the trial design. - During CT definition/reviews will decide appropriate TXPARM and TXVAL; Treatment duration may be controlled; For now, we just include good example values based on our experience
- Where are the details of the smoke regime defined/submitted today? (e.g., puff profile = Bell shaped puffing volumes; Puff Block = 50%, etc.)
- Smoke fraction? is this indicator of processing of material from smoke machine..we used Smoke Exposure System - ok?
- Incubate cells (37 ºC ±1 ºC, 90% ±10% humidity, and 5% ±1% CO2/air) - these are ranges, do we model for ranges?
Row | STUDYID | ASSAYID | DOMAIN | SETCD | | TXSEQ | TXPARMCD | TXPARM | TXVAL |
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1 | 123 | NRU | TX | 1-2-B(plate-col-row in the 96-well plate) | CSC-10(through SLS-200) | 1 | PLATENUM. (e.g., 1 or 2) | 1 | 1 |
2 | 123 | NRU | TX | 1-2-B | CSC-10 | 2 | WELLNUM (e.g., 1-A through 10-H) | Number representing the location of the well in a multiple-well plate | 2-B |
3 | 123 | NRU | TX | 1-2-B | CSC-10 | 4 | ITVTYPE(CT e.g, Product, positive control, negative control, vehicle control, solvent control) | type of intervention article | PRODUCT |
123 | NRU | TX | 1-2-B | CSC-10 | 5 | ITVCONC | intervention concentration | 50 | 123 | NRU | TX | 1-2-B | CSC-10 | 6 | ITVCONCU | intervention unit | ug/ml | 123 | NRU | TX | 1-2-B | CSC-10 | 7 | STRAIN | Strain/Substrain | Salmonella enterica enterica | 123 | NRU | TX | 1-2-B | CSC-10 | 8 | SPDEVID | Sponsor defined device identifier | PUFFMASTER3k | 123 | NRU | TX | 1-2-B | CSC-10 | 9 | DUREFID | Smoking Regime | Medium Intensity Regimen | 123 | NRU | TX | 1-2-B | CSC-10 | 10 | RUN | Assay run number | 1 | 123 | NRU | TX | 1-2-B | CSC-10 | 11 | SMPLID | Sample ID | 030001 | 123 | NRU | TX | 1-2-B | CSC-10 | 12 | SMKEXSYS | Smoke Exposure System | Cambridge filter pad, eluted in DMSO | 123 | NRU | TX | 1-2-B | CSC-10 | 13 | REPNUM | Replicate Number | 1 | 123 | NRU | TX | 1-2-B | CSC-10 | 14 | TRTDMIN | Treatment Duration Min | 47.5 | 123 | NRU | TX | 1-2-B | CSC-10 | 15 | TRTDTRG | Treatment Duration Target | 48 | 123 | NRU | TX | 1-2-B | CSC-10 | 16 | TRTDMAX | Treatment Duration Max | 48.5 | 123 | NRU | TX | 1-2-B | CSC-10 | 17 | TRTDU | Treatment Duration Unit | HOURS | 123 | NRU | TX | 1-2-B | CSC-10 | 18 | INCBTMP | Incubation Temperature | 37 | 123 | NRU | TX | 1-2-B | CSC-10 | 19 | INCBTMPU | Incubation Temperature Unit | C
| 123 | NRU | TX | 1-2-B | CSC-10 | 20 | MEDIA | Composition of Media | Sartorius HEK293 | 123 | NRU | TX | 1-2-B | CSC-10 | 21 | HUMID | Atmospheric Relative Humidity Percent | 90 | 123 | NRU | TX | 1-2-B | CSC-10 | 22 | ATMCO2 | Atmospheric CO2 Percent | 5 | 123 | NRU | TX | 1-2-B | CSC-10 | 23 | SPTOBID | Sponsor defined tobacco identifier | CIG01a | 123 | NRU | TX | 1-1-B | CSC-10 | 1 | PLATENUM. (e.g., 1 or 2) | 1 | 1 | 123 | NRU | TX | 1-1-B | CSC-10 | 2 | WELLNUM (e.g., 1-A through 10-H) | Number representing the location of the well in the 96-well plate | 1-A | 123 | NRU | TX | 1-1-B | CSC-10 | 3 | INTRVN | name of the intervention article | Cigarette Smoke Condensate | 123 | NRU | TX | 1-1-B | CSC-10 | 4 | ITVTYPE(CT e.g, Product, positive control, negative control) | type of intervention article | PRODUCT | 123 | NRU | TX | 1-1-B | CSC-10 | 5 | ITVCONC | intervention concentration | 10 | 123 | NRU | TX | 1-1-B | CSC-10 | 6 | ITVCONCU | intervention unit | ug/ml | 123 | NRU | TX | 1-1-B | CSC-10 | 7 | STRAIN | Strain/Substrain | Salmonella enterica enterica | 123 | NRU | TX | 1-1-B | CSC-10 | 8 | SPDEVID | Sponsor defined device identifier | PUFFMASTER3k | 123 | NRU | TX | 1-1-B | CSC-10 | 9 | DUREFID | Smoking Regime | Medium Intensity Regimen | 123 | NRU | TX | 1-1-B | CSC-10 | 10 | RUN | Assay run number | 1 | 123 | NRU | TX | 1-1-B | CSC-10 | 11 | SMPLID | Sample ID | 030001 | 123 | NRU | TX | 1-1-B | CSC-10 | 12 | SMKEXSYS | Smoke Exposure System | Cambridge filter pad, eluted in DMSO | 123 | NRU | TX | 1-1-B | CSC-10 | 13 | REPNUM | Replicate Number | 1 | 123 | NRU | TX | 1-1-B | CSC-10 | 14 | TRTDMIN | Treatment Duration Min | 47.5 | 123 | NRU | TX | 1-1-B | CSC-10 | 15 | TRTDTRG | Treatment Duration Target | 48 | 123 | NRU | TX | 1-1-B | CSC-10 | 16 | TRTDMAX | Treatment Duration Max | 48.5 | 123 | NRU | TX | 1-1-B | CSC-10 | 17 | TRTDU | Treatment Duration Unit | HOURS | 123 | NRU | TX | 1-1-B | CSC-10 | 18 | INCBTMP | Incubation Temperature | 37 | 123 | NRU | TX | 1-1-B | CSC-10 | 19 | INCBTMPU | Incubation Temperature Unit | C
| 123 | NRU | TX | 1-1-B | CSC-10 | 20 | MEDIA | Composition of Media | Sartorius HEK293 | 123 | NRU | TX | 1-1-B | CSC-10 | 21 | HUMID | Atmospheric Relative Humidity Percent | 90 | 123 | NRU | TX | 1-1-B | CSC-10 | 22 | ATMCO2 | Atmospheric CO2 Percent | 5 | 123 | NRU | TX | 1-1-B | CSC-10 | 23 | SPTOBID | Sponsor defined tobacco identifier | CIG01a | ... | ... | 123 | NRU | TX | 1-10-H | SLS-10 | PLATENUM | Plate number | 1 | 123 | NRU | TX | 1-10-H | SLS-10 | WELLNUM | Number representing the location of the well in the 96-well plate | 10-H | 123 | NRU | TX | 1-10-H | SLS-10 | INTRVN | name of the intervention article | sodium laurel sulfate | 123 | NRU | TX | 1-10-H | SLS-10 | ITVTYPE | type of intervention article | POSITIVE CONTROL | 123 | NRU | TX | 1-10-H | SLS-10 | ITVCONC | intervention concentration | 200 | 123 | NRU | TX | 1-10-H | SLS-10 | ITVCONCU | intervention unit | ug/ml | ... | ... | 123 | NRU | TX | 2-10-H | SLS-10 | PLATENUM | Plate number | 2 | 123 | NRU | TX | 2-10-H | SLS-10 | WELLNUM | Number representing the location of the well in the 96-well plate | 10-H | 123 | NRU | TX | 2-10-H | SLS-10 | INTRVN | name of the intervention article | sodium laurel sulfate | 123 | NRU | TX | 2-10-H | SLS-10 | ITVTYPE | type of intervention article | POSITIVE CONTROL | 123 | NRU | TX | 2-10-H | SLS-10 | ITVCONC | intervention concentration | 200 | 123 | NRU | TX | 2-10-H | SLS-10 | ITVCONCU | intervention unit | ug/ml | ... | ... | Expand |
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title | ei.xpt Entity Identifiers (dm-like) |
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- Entity IDs are unique within the assay (and a study can have many assays)
- Replicates vs. Run
- need planned (ei.xpt) separate from the actual (gt.xpt)
- If tests run at the same time, they are replicates and are assigned the same RUNID
- If tests are run at separate times, they are runs and the RUNIDs are distinct
- Different runs would be expected to have different ENID and GTDTC values. In ei.xpt, these are distinguished by different RUNID values.
- Entities that are replicates of each other would be expected to
- have different ENID values
- be in the same trial set (SETCD values)
- have the same RUNID values
Row | STUDYID | ASSAYID | DOMAIN | ENID (Entity ID) | SETCD (from TX) | RUNID | REPLCTID (Replicate Number) | PLATEID (Plate ID) | COLID (Column number) | ROWID (Row number) |
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123 | NRU | EI | 1-2-B | 1-2-B | 1 | 1-8-3 (plate - col- row) | |
Dataset wrap |
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Certain data (Absorbance Reading and Background Corrected Absorbance Reading) are not shown in the sample report table above but are included here for completeness of the NRU assay. Rowcaps |
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Rows 1-3: | Show the experimental unit data for GTREFID 1-3-B. | Rows 4-6: | Show the experimental unit data for GTREFID 1-3-C. | Rows 7-9: | Show the data for the entire trial set, GTREFID=1-3. | Rows 10-12: | Show the experimental unit data for GTREFID 1-10-G | Rows 13-15: | Show the data for the entire trial set, GTREFID=1-10 | Rows 16-18: | Show the experimental unit data for GTREFID 2-10-G. | Rows 19-21: | Show the data for the entire trial set, GTREFID=2-10 | Row 22: | Shows the data for the entire assay, GTREFID=123NRU. |
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Dataset2 |
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Row | STUDYID | DOMAIN | GTSEQ | GTREFID | GTTESTCD | GTTEST | GTORRES | GTORRESU | GTCOLSRT | GTSTRESC | GTSTRESN | GTSTRESU |
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1 | 123 | GT | 1 | 1-3-B | ABSORB | Absorbance Reading | 1.7 |
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| 1.7 | 1.7 |
| 2 | 123 | GT | 2 | 1-3-B | BKCABS | Background Corrected Absorbance Reading | 1.6 |
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| 1.6 | 1.6 |
| 3 | 123 | GT | 3 | 1-3-B | RELABS | Relative Absorbance Reading | 77.7 |
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| 77.7 | 77.7 |
| 4 | 123 | GT | 4 | 1-3-C | ABSORB | Absorbance Reading | 1.8 |
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| 1.8 | 1.8 |
| 5 | 123 | GT | 5 | 1-3-C | BKCABS | Background Corrected Absorbance Reading | 1.7 |
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| 1.7 | 1.7 |
| 6 | 123 | GT | 6 | 1-3-C | RELABS | Relative Absorbance Reading | 77.4 |
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| 77.4 | 77.4 |
| 7 | 123 | GT | 7 | 1-3 | RELABS | Relative Absorbance Reading | 78.2 | % | MEAN | 78.2 | 78.2 | % | 8 | 123 | GT | 8 | 1-3 | RELABS | Relative Absorbance Reading | 2.9 | % | STANDARD DEVIATION | 2.9 | 2.9 | % | 9 | 123 | GT | 9 | 1-3 | RELABS | Relative Absorbance Reading | 3.6 |
| COEFFICIENT OF VARIANCE | 3.6 | 3.6 |
| 10 | 123 | GT | 10 | 1-10-G | ABSORB | Absorbance Reading | 0.7 |
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| 0.7 | 0.7 |
| | 123 | GT | 11 | 1-10-G | BKCABS | Background Corrected Absorbance Reading | 0.6 |
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| 0.6 | 0.6 |
| 12 | 123 | GT | 12 | 1-10-G | RELABS | Relative Absorbance Reading | 8.57 |
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| 8.57 | 8.57 |
| 13 | 123 | GT | 13 | 1-10 | RELABS | Relative Absorbance Reading | 8.94 | % | MEAN | 8.94 | 8.94 |
| 14 | 123 | GT | 14 | 1-10 | RELABS | Relative Absorbance Reading | 2.72 | % | STANDARD DEVIATION | 2.72 | 2.72 |
| 15 | 123 | GT | 15 | 1-10 | RELABS | Relative Absorbance Reading | 30.5 |
| COEFFICIENT OF VARIANCE | 30.5 | 30.5 |
| 16 | 123 | GT | 16 | 2-10-G | ABSORB | Absorbance Reading | 0.9 |
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| 17 | 123 | GT | 17 | 2-10-G | BKCABS | Background Corrected Absorbance Reading | 0.8 |
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| 18 | 123 | GT | 18 | 2-10-G | RELABS | Relative Absorbance Reading | 6.30 |
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| 6.30 | 6.30 |
| 19 | 123 | GT | 19 | 2-10 | RELABS | Relative Absorbance Reading | 5.91 | % | MEAN | 5.91 | 5.91 |
| 20 | 123 | GT | 20 | 2-10 | RELABS | Relative Absorbance Reading | 0.83 | % | STANDARD DEVIATION | 0.83 | 0.83 |
| 21 | 123 | GT | 21 | 2-10 | RELABS | Relative Absorbance Reading | 14.1 |
| COEFFICIENT OF VARIANCE | 14.1 | 14.1 |
| 22 | 123 | GT | 22 | 123NRU | | Effective Concentration of 50 Percent Cytotoxicity | 123 | ug/ml |
| 123 | 123 |
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123 | NRU | EI | 1-3-B | 1-3-B | 1 | Expand |
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title | gt.xpt (similar to LB) |
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Image Removed . Image Removed Image RemovedImage Removed *** Lou Ann: new pictures with blank media on perimeter Data values in gt.xpt will be from 2b (1a), 2c (2b), 10g (not 10H) on both plates |
Row | STUDYID | ASSAYID | DOMAIN | ENID | GTSEQ | GTTESTCD | GTTEST | GTORRES | GTORRESU | GTSTRESC | GTSTRESN | GTSTRESU |
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1 | 123 | NRU | GT | 1-2-B | 1 | RELABS | Relative Absorbance Reading | 77.7 | ug/ml | 77.7 | 77.7 | ug/ml |
2 | 123 | NRU | GT | 1-2-C | 1 | RELABS | Relative Absorbance Reading | 77.4 | ug/ml | 77.4 | 77.4 | ug/ml |
... | 80 | 123 | NRU | GT | 1-10-H | 1 | RELABS | Relative Absorbance Reading | 8.57 | ug/ml | 8.57 | 8.57 | ug/ml |
... | ... | 160 | 123 | NRU | GT | 2-10-H | 1 | RELABS | Relative Absorbance Reading | 6.30 | ug/ml | 6.30 | 6.30