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gt.xpt, genetic toxicology in vitro test results TOBA-14 - Getting issue details... STATUS - Findings. One record per test per observation time per entity, Tabulation.

Variable Name

Variable Label

Type

Controlled Terms, Codelist, or Format

Role

CDISC Notes

Core

STUDYID  (1)

Study Identifier

Char


Identifier

Unique identifier for a study.

Req

ASSAYID

Assay Identifier

Char


Identifier

Sponsor defined identifier for the assay within the study.

Req

DOMAIN (2)

Domain Abbreviation

Char

GT            

Identifier

Two-character abbreviation for the domain.

Req

SETCD (1)

Set Code

Char


Identifier

Short name of a specific Trial Set to which the results are attributed. Maximum size is 8 characters.

Exp

EUID (2)

Experimental Unit Identifier

Char


Identifier

Experimental Unit Identifier is the unit to which the treatment is applied.  Experimental Unit Identifiers are unique within an assay. 

Exp

OBUID (3)

Observation Unit Identifier

Char


Identifier

Observation Unit identifier is the unit on which the response is measured.  Observation Unit Identifiers are unique within an Experimental Unit.

Exp

GTSEQ (9)

Sequence Number

Num


Identifier

The sequence number must be unique for each record within a domain.

Sequence number given to ensure uniqueness of records within a domain. May be any valid number.

Req

GTGRPID (10)

Group ID

Char


Identifier

Optional group identifier, used to link together a block of related records within a subject in a domain.

Perm

GTREFID (11)Reference IDChar
IdentifierA sequence of characters used to uniquely identify a source of information. Examples: lab specimen ID, petri dish ID, flask ID, well IDReq

GTTESTCD (1)

Lab Test or Examination Short Name

Char

(GTTESTCD)

Topic

Short name of the measurement, test, or examination described in GTTEST. It can be used as a column name when converting a dataset from a vertical to a horizontal format. The value in GVTESTCD cannot be longer than 8 characters, nor can it start with a number (e.g., “1TEST” is not valid). GVTESTCD cannot contain characters other than letters, numbers, or underscores. Examples: RVERT, CYTOTOX.

Req

GTTEST (2)

Lab Test or Examination Name

Char

(GTTEST)

Synonym Qualifier

Long name for GTTESTCD. The value in GTTEST cannot be longer than 40 characters. Examples: Revertants, Cytotoxicity.

Req

GTORRES (28)

Result or Findings as Collected

Char


Result Qualifier

Result of the measurement or finding as originally received or collected.

Exp

GTORRESU (29)

Unit of the Original Result

Char

(UNIT)

Variable Qualifier

The unit for the original result. The unit of the original result should be mapped to a synonymous unit on the Controlled Terminology list.

Exp

GTCELLEV

Number of Cells Evaluated

Num


Result Qualifier

The number of cells evaluated.

Perm

GTCOLSRT (32)

Collected Summary Result Type

Char

(COLSTYP)

Variable Qualifier

Used to indicate the type of collected summary result. For example, MAXIMUM, MINIMUM, and MEAN

Perm

GTSTRESC (37)

Standardized Result in Character Format

Char

New code list needed


Result Qualifier

Contains the result value for all findings, copied or derived from GTORRES in a standard format or standard units. GTSTRESC should store all results or findings in character format; if results are numeric, they should also be stored in numeric format in GTSTRESN. For example, if a test has results NONE, NEG, and NEGATIVE in GTORRES and these results effectively have the same meaning, they could be represented in standard format in GTSTRESC as NEGATIVE. For other examples, see general assumptions.

Exp

GTSTRESN (39)

Standardized Result in Numeric Format

Num


Result Qualifier

Used for numeric results or findings in standard format; contains the numeric form of GTSTRESC. GTSTRESN should store all numeric test results or findings.

Exp

GTSTRESU (40)

Unit of the Standardized Result

Char

(UNIT)

Variable Qualifier

Standardized unit used for GTSTRESC, GTSTRESN, GTSTRLO, and GTSTRHI.

Exp

GTSTAT (61)

Completion Status

Char

(ND)

Record Qualifier

Used to indicate when a test is not done or result is missing. Should be null if a result exists in GTORRES.

Perm

GTREASND (62)

Reason Not Done

Char


Record Qualifier

Describes why GTSTAT is NOT DONE, such as BROKEN EQUIPMENT or SPECIMEN LOST.

Perm

GTSPEC (66)

Specimen Material TypeChar
Record Qualifier

The type of sample material taken from a biological entity. "SERUM", "PLASMA", "URINE", "DNA", "RNA"

Perm

GTSPCCND (68)

Specimen Condition

Char

?

Record Qualifier

Free or standardized text describing the condition of the specimen. Example: PRECIPITATION PRESENT, CONTAMINATION PRESENT, etc.  If multiple conditions are present on a sample, concatenate the values with a semicolon and no spaces as a separator

Perm

GTSPCUFL (69)

Specimen Usability for the Test

Char

(NY)

Record Qualifier

Describes the usability of the specimen for the test. Should be N if the specimen is not usable; otherwise it should be null.

Perm

GTMETHOD (74)

Method of Test or Examination

Char


Record Qualifier

Method of the test or examination. Examples: MANUALLY COUNTED, INSTRUMENT COUNTED

Exp

GTRUNID (75)

Run ID

Char


Record Qualifier

A sequence of characters used to uniquely identify a particular run of a test on a particular batch of samples.

Perm

GTEXCLFL (95)

Exclusion Flag

Char

(NY)

Record Qualifier

Y if the result should be excluded from all calculations, otherwise null.

Perm

GTREASEX (96)

Reason for Exclusion

Char


Record Qualifier

The reason the result should be excluded from all calculations. Used only when GTEXCLFL is Y.

Perm

GTDTC 

Date/Time of Collection

Char

ISO 8601 datetime or interval

Timing

The date or date and time of the assessment or the specimen or data collection from the subject, represented in a standardized character format. For an Ames test, this is the date the bacterial culture is plated.

Perm


6.3.?.1  ASSUMPTIONS FOR GENETIC TOXICOLOGY IN VITRO TEST RESULTS (GT) DOMAIN MODEL

  1. GT Definition: This domain captures in vitro data collected by the lab executing the study or received from a provider.  This domain is designed for exchanging sample (entity) level data for the following in vitro tests: Neutral Red Cytotoxity Assay, Bacterial Reverse Mutation Assay, Mammalian Cell Gene Mutation Assay, and Micronucleus Assay.  Other in vitro tests have not yet been modeled in this version of this domain.

  2. Meaning of null values in SETCD, EUID, and OBUID:
    1. Records with the same EUID but different RUNID refer to separate entities (e.g., a unique tube, plate, or well) being observed.
    2. If the EUID is null, the OBUID must be null and the result applies to the trial set.
    3. Records with the same OBUID but different RUNID refer to separate entities (e.g., a unique tube, plate, or well) being observed.
    4. If the OBUID is null, the result applies to the experimental unit.
    5. If SETCD is null, both the EUID and OBUID must be null and the result applies to the assay.
  3. Within a run, the OBUID is unique within an experimental unit and uniquely identifies the entity on which the observation is made (e.g., a unique tube, plate, or well).
  4. Results Definition:
    1. GTSTRESC and the corresponding numeric GTSTRESN should generally be used to represent standardized format of original results.
    2. GTSTAT and GTREASND are Permissible and used to indicate when a test was not completed. In these cases GTSTAT should contain “NOT DONE”; GTORRES, GTSTRESC, and GTSTRESN should be null; and GTREASND should contain the reason for not completing the test.
  5. Other Assumptions:
    1. The discussion in Section 4.5.1.3 concerning TESTS NOT DONE does not apply to this domain.
    2. GTEXCLFL and GTREASEX are Permissible and used to indicate when a test is to be excluded from further analysis. In these cases GTREASEX should contain the reason for exclusion.




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