How to Design a Custom SDTM Domain for Nonclinical Data ... · How to Design a Custom SDTM Domain for Nonclinical Data PhUSE Standards Roadmap Team Contents Abstract: 1 Using the

1 of 35 Authored by the PhUSE Nonclinical Roadmap team, December 2014.

How to Design a Custom SDTM Domain for Nonclinical Data

PhUSE Standards Roadmap Team

Contents Abstract: 1

Using the “How to Design a Domain” resource 2

DOMAIN TABLE SKELETON – XX 5

Appendix 1. Table of SDTM Variable Categories and Subcategories 13

Appendix 2. Use Cases for the Custom Domain Resource 14

Abstract:

Data Standards are being developed to convey complex clinical and nonclinical data in a standard form

across organizations and for regulatory submissions. CDISC SEND is a nonclinical standard for general

toxicology studies and carcinogenicity studies. The SEND standard is currently being expanded to include

reproductive and developmental toxicology studies and safety pharmacology studies. Though study

designs for many nonclinical studies have uniform design and often capture similar endpoints, some design

elements and study endpoints may have a more unique quality that has not been specifically considered in

the standard. The science of study conduct and data interpretation allows data to be captured in various

ways across studies. Providing a dataset standard for a given data type will end up being a compromise of

the different ways of collecting this data. This built in flexibility in the dataset standard will now in every

instance be subject to interpretations of the tenets of the standard, and approaches to its use may be so

creative that similar data across studies may be tabulated in multiple ways. In such cases, data loses a

standard quality. The Standards Roadmap Team created a decision tree to guide a data-driven decision-

making for capturing not-yet standardized data types in a standard dataset. The intent is to streamline and

improve uniformity in the interpretation of the tenets of the SDTM standard and thereby providing a

consistent way of creating a standard domain structure specifically suited for the data belonging to a

findings general observation class.


Using the “How to Design a Domain” resource

The purpose of this resource is to guide users toward appropriate variables that will accommodate data

types that are not specified in the standard. The primary reference is the decision tree which will guide

users on which domain variables are most appropriate for their data types. The decision tree is directly

below this section (Figure 1) and is also provided as a Visio file that accompanies this resource. Users

should begin at the top left of the decision tree at the category “Core Dataset Structure” and follow the

“swim lane” going right across the decision tree for this category of variables. The categories on the

decision tree have corresponding color-coding on the Domain Table, which is a supplemental reference

document that provides more detail on the nature of variables. The questions in the decision tree will

guide the user as to when groups of variables are needed for their particular data. When users encounter a

grouping of variables on the decision tree, they should then refer to the Domain Table “Core” column to

determine which variables are considered required, expected or permissible for their data type. After

completing the decisions for a category (i.e. traveling to the end of a lane) the user should go to the lane

directly below the one they completed and follow the decision tree (left to right) across that lane. The user

should consider each category (i.e. Core Dataset Structure, Object Identifiers etc.) and it is essential to use

each category in a dataset. In other words, all categories of variables are essential to a dataset but the

decision tree will guide the user to select the relevant groups of variables within these categories. Some

guidance for selecting variables within a group is provided in the “Core (within a variable group)” column,

however the fine tuning of the domain structure should reflect the data need.

If you answer both yes and no to some of the questions, you are likely dealing with more than one data

type in mind. Have each of the data types go through the decision tree and decide in the end if the record

structure is similar enough to allow for collapsing the two resulting domain structures into one. This is not

recommended if the domain structures have different Object Identifiers, Test Variables or Timing Variables.

The CDISC SDTM model allows for addition of an extensive number of variables to a findings observation

class domain. The Standards Roadmap Team has assessed these variables from a nonclinical perspective

and selected the ones considered most applicable for nonclinical studies. These are the variables presented

in the domain table below and those that you are guided through in the decision tree. If you find that there

is an additional need for further variables to accurately reflect the data, it is to the user’s discretion to add

SDTM variables allowed for a Findings General Observation Class domain from the SDTM while maintaining

the proper sequence of all variables as described in SDTM.

The data in scope for this resource is collected data from nonclinical studies that would be expected to be

modelled as findings data and which can be supplemented to a data package based on CDISC SEND version

3.0. This resource has not been applied to clinical data and such use is not recommended. Further

development is necessary to address clinical needs.

The domain table below should not be read without the decision tree. From a familiarity point of view, the

“Core” column in the domain table below is not referring to a requirement on a domain level, but a

requirement on a variable grouping level. Example: If the object being assessed is a group of subjects, then

you are prompted in the decision tree to add the “OI-1” variables. You should not also add “OI-2” or “OI-3”

variables if they are indicated as required in the “Core” column. Only when the decision tree warrants you

to add a group of variables, should you then refer to the “Core” column for further guidance on expectancy


within the group of variables. Once you have settled with the right groups of variables, the sequence must

match that of the domain table below. Permissible variables that you have gained as part of a group can be

freely deleted if there is no use for them for your particular data, however required and expected variables

must be included due to the answers you have provided in the decision tree. The required and some of the

expected variables will be the natural keys in your new domain. The natural keys are those variables that

collectively provide a unique identification of every record in the dataset and they define the record

structure. Note that the expectancy of the variables is not intended to reflect any published SEND or SDTM

domain, but rather serve as a guide towards common scenarios for how to tabulate nonclinical data.

Appendices are provided as general reference material and as confirmation that the output from the

resource follows basic SDTM concepts. Appendix 1 is a tabular view of the categories, subcategories and

variables that are used in this resource. The list in Appendix 1 serves as a general reference to ensure that

users considered all variables within each subcategory. Several use cases are provided in Appendix 2 to

demonstrate how unmodeled data can be modeled using this resource

As part of developing this resource the PhUSE Nonclinical Roadmap team looked into current published

validation rules to see if some guidance could be provided on how to verify that fundamentals of the

standard are maintained in the new custom domain. The analysis of validation rules resulted in a non-

exhaustive list of checks from the public domain which can be considered key elements for any SDTM

findings dataset. The analysis outcome is presented as a separate Excel file and can be found at

http://www.phusewiki.org/wiki/index.php?title=WG6_Nonclinical_-_Standardization_Roadmap.

Additional conformance rules for SDTM datasets can be found at:

http://www.phusewiki.org/wiki/index.php?title=Representing_CDISC_Conformance_Checks.

http://www.phusewiki.org/wiki/index.php?title=WG6_Nonclinical_-_Standardization_Roadmap

http://www.phusewiki.org/wiki/index.php?title=Representing_CDISC_Conformance_Checks


Figure 1 – Decision Tree


DOMAIN TABLE SKELETON – XX

xx.xpt, - Findings. Tabulation, Record structure will depend on the outcome of the decision tree.

Decision based adding of variables (see decision

tree)

SDTM / SEND definitions and rules for the population of the variables

Variable category Variable group Core

(within

variable

group)

Variable

Name

Variable Label Type Controlled

Terms,

Codelist, or

Format

Role CDISC Notes

Core Dataset

structure

Mandatory Req STUDYID Study Identifier Char Identifier Unique identifier for a study.

Core Dataset

structure

Mandatory Req DOMAIN Domain

Abbreviation

Char XX Identifier Two-character abbreviation for the domain. Refer to

CDISC SDTMIG and SENDIG for reserved domain

codes. Domain codes starting with “X”, “Y” and “Z”

are always considered

Object Identifier OI-2 Req USUBJID Unique Subject

Identifier

Char Identifier Identifier used to uniquely identify a subject across all

studies for all application or submissions involving the

product.

Object Identifier OI-1 Req POOLID Pool Identifier Char Identifier Pooling Identifier for Samples. Either USUBJID or

POOLID must be populated.

Core Dataset

structure

Mandatory Req --SEQ Sequence

Number

Num Identifier Sequence number given to ensure uniqueness of

subject records within a domain. May be any valid

number.

Object Identifier OI-3 Perm --REFID Reference

Identifier

Char Identifier Optional internal or external identifier such as lab

specimen ID, or UUID for an ECG waveform or a

medical image.

Core Dataset

structure

CD-1 Perm --SPID Sponsor-

Defined

Identifier

Char Identifier Sponsor-defined reference number. Perhaps preprinted

as an explicit line identifier or defined in the sponsor’s

operational database. Example: Line number on the

Lab page.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Test Variables Mandatory Req --TESTCD Measurement,

Test or

Examination

Short Name

Char Controlled

terminology

is expected

Topic Short name of the measurement, test, or examination

described in --TEST. It can be used as a column name

when converting a dataset from a vertical to a

horizontal format. The value in --TESTCD cannot be

longer than 8 characters, nor can it start with a number

(e.g., “1TEST” is not valid). LBTESTCD cannot

contain characters other than letters, numbers, or

underscores.

Test Variables Mandatory Req --TEST Measurement,

Test or

Examination

Name

Char Controlled

terminology

is expected

Synonym

Qualifier

Long name for --TESTCD. The value in LBTEST

cannot be longer than 40 characters.

Test Variables TV-1 Exp

--CAT Measurement,

Test or

Examination

Category

Char Controlled

terminology

is expected

Grouping

Qualifier

Used to define a category of related tests across

subjects.

Test Variables TV-1 Perm --SCAT Measurement,

Test or

Examination

Subcategory

Char Grouping

Qualifier

A further categorization of a test category

Object Identifier OI-4 Perm --POS Position of

Subject during

Observation

Char (POSITIO

N)

Record

Qualifier

Position of the subject during a measurement or

examination. Examples: SUPINE, STANDING,

SITTING.

Result Variables Mandatory Exp --ORRES Result or

Finding as

Collected

Char Result

Qualifier

Result of the measurement or finding as originally

received or collected.

Results Variables RV-3 Exp --ORRESU 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.

Results Variables RV-4 Perm

--ORNRLO Reference

Range Lower

Limit-Orig Unit

Char Variable

Qualifier

Lower end of reference range used at the time of

collection, in original units.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Results Variables RV-4 Perm --ORNRHI Reference

Range Upper

Limit-Orig Unit

Char Variable

Qualifier

Upper end of reference range used at the time of

collection, in original units.

Results Variables Mandatory Exp --STRESC Standardized

Result in

Character

Format

Char Controlled

terminology

is expected

Result

Qualifier

Contains the result value for all findings, copied or

derived from --ORRES in a standard format or

standard units. --STRESC should store all results or

findings in character format; if results are numeric,

they should also be stored in numeric format in --

STRESN.

Results Variables RV-3 Exp --STRESN Standardized

Result in

Numeric Format

Num Result

Qualifier

Used for continuous or numeric results or findings in

standard format; contains the numeric form of --

STRESC.

Results Variables RV-3 Exp --STRESU Unit of the

Standardized

Result


Qualifier

Standardized unit used for --STRESC and --STRESN.

Results Variables RV-4 Perm --STNRLO Reference

Range Lower

Limit-Std Unit

Num Variable

Qualifier

Lower end of reference range for continuous or

numeric standardized results (--STRESN) represented

in standardized units.

Results Variables RV-4 Perm --STNRHI Reference

Range Upper

Limit-Std Unit

Num Variable

Qualifier

Upper end of reference range for continuous or

numeric standardized results (--STRESN) represented

in standardized units.

Results Variables RV-4 Perm --STNRC Reference

Range for Char

Rslt-Std Unit

Char Variable

Qualifier

Reference range for results stored in --STRESC that

are character in ordinal or categorical scale. Example:

Negative to Trace.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Results Variables RV-4 Perm --RIND Reference

Range Indicator

Char Variable

Qualifier

Indicates where value falls with respect to reference

range defined by --ORNRLO and --ORNRHI, by --

STRNRLO and --STNRHI, or by --STNRC. Examples:

NORMAL, ABNORMAL, HIGH, LOW. This should

not be used to indicate biological significance.

Sponsors should specify in the study metadata

(Comments column in the data definition file) whether

LBNRIND refers to the original or standard reference

ranges and results.

Results Variables RV-2 Exp --RESCAT Result Category Char Controlled

terminology

is expected

Variable

Qualifier

Used to categorize the result of a finding post

collection.

Result Variables Mandatory Perm --STAT Completion

Status

Char (ND) Record

Qualifier

Used to indicate when a test is not done or result is

missing. Should be null if a results exists in --ORRES.

Result Variables Mandatory Perm --REASND Reason Not

Done

Char Record

Qualifier

Describes why --STAT is NOT DONE, such as

BROKEN EQUIPMENT or SICK ANIMAL.

Core Dataset

structure

CD-1 Perm --XFN External File

Name

Char Record

Qualifier

Filename for an external file associated with the result

Test Variables TV-3 Perm --NAM Vendor Name Char Record

Qualifier

Name or identifier of the laboratory or vendor that

provided the test results.

Object Identifier OI-3 Exp --SPEC Specimen

Material Type

Char (SPEC) Record

Qualifier

Defines the type of tissue, organ, or fluid specimen

used as the object for the finding. Examples: GLAND,

ADRENAL; KIDNEY; VESSEL, LYMPHATIC.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Object Identifier OI-3 Exp --ANTREG Anatomical

Region of

Specimen

Char Variable

Qualifier

Defines the specific anatomical or biological region of

a tissue, organ specimen or the region from which the

specimen was obtained, such as a section or part of

what is defined in the --SPEC variable. If the

anatomical region is not included in the specimen

description --SPEC, it may be included in this variable.

This field can be a combination of terms where needed.

This field can be null if not applicable. Examples:

CORTEX, MEDULLA, MUCOSA, SEROSA, ISLET,

ZONA FASICULATA, ZONA RETICULARIS,

CRANIAL, MEDIAN, ACCESSORY, SPINAL,

LUMBAR, FRONTAL.

Object Identifier OI-3 Perm --SPCCND Specimen

Condition

Char Variable

Qualifier

Free or standardized text describing the condition of

the specimen. Example: AUTOLYZED,

HEMOLYZED, ICTERIC, LIPEMIC, etc.

Object Identifier OI-3 Perm --SPCUFL Specimen

Usability for the

Test

Char (NY) Variable

Qualifier

Describes the usability of the specimen for the test.

Example: N = the specimen is not usable; otherwise

null.

Object Identifier OI-5 Perm --LOC Location

associated with

a result or

finding

Char Record

Qualifier

Anatomical location associated with the test. Example

rectal for temperature.

Object Identifier OI-3 Perm --LAT Specimen

Laterality

within Subject

Char (LAT) Variable

Qualifier

Qualifier for laterality of the specimen within the

subject for paired specimens. Examples: LEFT,

RIGHT, BILATERAL.

Object Identifier OI-3 Perm --DIR Specimen

Directionality

within Subject

Char (DIR) Variable

Qualifier

Qualifier for directionality of the specimen within the

subject. Examples: DORSAL, PROXIMAL.

Object Identifier OI-3 Perm --PORTOT Portion or

Totality

Char (PORTOT) Variable

Qualifier

Qualifier for anatomical location or specimen further

detailing the portion or totality which means

arrangement of, or apportioning of, for example,

ENTIRE, SINGLE, SEGMENT, MANY.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Test Variables TV-2 Perm --

METHOD

Method of Test

or Examination

Char Record

Qualifier

Method of the test or examination.

Object Identifier OI-4 Perm --CSTATE Consciousness

State

Char (CSTATE) Record

Qualifier

The consciousness state of the subject at the time of

measurement.

Examples: CONSCIOUS, SEMI-CONSCIOUS,

UNCONSCIOUS.

Result Variables RV-3 Exp --BLFL Baseline Flag Char (NY) Record

Qualifier

A baseline indicator may be used to calculate

differences or changes from baseline. Value should be

Y or null. The baseline flag is sponsor-defined.

Object Identifier OI-4 Perm --FAST Fasting Status Char (NY) Record

Qualifier

Indicator used to identify fasting status. Null if not

relevant.

Test Variables TV-3 Perm --EVAL Evaluator Char Record

Qualifier

Role of the person who provided the evaluation. Used

only for results that are subjective (e.g., assigned by a

person or a group). Should be null for records that

contain collected or derived data. Examples:

RESPONSIBLE SCIENTIST, PRINCIPAL

INVESTIGATOR, PEER

REVIEWER.

Results Variables RV-1 Perm --SEV Severity Char (SEV) Record

Qualifier

Describes the severity or intensity of a particular

finding.

Test Variables TV-2 Perm --LLOQ Lower Limit of

Quantitation

Num Variable

Qualifier

Indicates the lower limit of quantitation for an assay.

Units will be those used in --STRESU.

Test Variables TV-2 Perm --ULOQ Upper Limit of

Quantitation

Num Variable

Qualifier

Indicates the upper limit of quantitation for an assay.

Units will be those used in --STRESU.

Results Variables Mandatory Perm --EXCLFL Exclusion Flag Char (NY) Record

Qualifier

Y if the result should be excluded from all calculations,

otherwise null.

Results Variable Mandatory Perm --REASEX Reason for

Exclusion

Char Record

Qualifier

The reason the result should be excluded from all

calculations. Used only when --EXCLFL is Y.

Timing Variables Mandatory Exp VISITDY Planned Study

Day

Num Timing This is the planned study day of collection.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Timing Variables TM-1 Exp

--DTC Date/Time of

Test

Char ISO 8601 Timing Date/time of the measurement, test or observation in

IS0 8601 format.

Timing Variables TM-3 Exp --STDTC Start Date/Time

of Test

Char ISO 8601 Timing Date/time of the start of the measurement, test, or

observation in ISO 8601 format. Should be populated

only for continuous sample collection.

Timing Variables TM-3 Perm --ENDTC End Date/Time

of Test

Char ISO 8601 Timing Date/time of the end of the measurement, test, or

observation in ISO 8601 format. Should be populated

only for continuous sample collection.

Timing Variables TM-1 Exp --DY Study Day of

Test

Num Timing Study day of the measurement, test or observation, in

integer days. The algorithm for calculations must be

relative to the sponsor-defined RFSTDTC variable in

the Demographics (DM) domain.

Timing Variables TM-3 Exp --STDY Study Day of

Start of Test

Num Timing Study day of the start of the measurement, test, or

observation, in integer days. The algorithm for

calculations must be relative to the sponsor-defined

RFSTDTC variable in the Demographics (DM) domain.

Timing Variables TM-3 Perm --ENDY Study Day of End

of Test

Num Timing Study day of the end of the measurement, test, or

observation, in integer days. The algorithm for

calculations must be relative to the sponsor-defined

RFSTDTC variable in the Demographics (DM) domain.

Timing Variables TM-3 Perm --DUR Duration of Test Char ISO 8601 Timing Collected duration of a measurement, test, or

observation, represented in ISO8601 format. This

should not be used to report a derived duration.

Timing Variables TM-2 Exp --TPT Planned Time

Point Name

Char Timing Text description of the planned time of the

measurement, test or observation.

This may be represented as an elapsed time relative to

a fixed reference point, such as time of last dose. See

LBTPTNUM and LBTPTREF. Examples: Start, 5 min

post.

Timing Variables TM-2 Exp --TPTNUM Planned Time

Point Number

Num Timing Numerical version of --TPT to aid in sorting.



tree)



(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role CDISC Notes

Timing Variables TM-2 Exp --ELTM Planned Elapsed

Time from Time

Point Ref

Char ISO 8601 Timing Planned elapsed time (in ISO 8601 format) relative to a

planned fixed reference (--TPTREF). This variable is

useful where there are repetitive measures. Not a clock

time or a date time variable. Represented as an ISO

8601 duration. Examples: “- P15M” to represent the

period of 15 minutes prior to the reference point

indicated by LBTPTREF, or “P8H” to represent the

period of 8 hours after the reference point indicated by

LBTPTREF.

Timing Variables TM-2 Exp --TPTREF Time Point

Reference

Char Timing Name of the fixed reference point referred to by --

ELTM, if used for LBTPTNUM, and LBTPT.

Examples: PREVIOUS DOSE, PREVIOUS MEAL.

Timing Variables TM-2 Exp --RFTDTC Date/Time of

Reference Time

Point

Char ISO 8601 Timing Date/time of the reference time point, --TPTREF

Timing Variables TM-4 Perm --EVLINT Evaluation

Interval

Char ISO 8601 Timing Duration of interval associated with an observation

such as a finding --TESTCD, represented in ISO 8601

character format. Example: -P2M to represent a period

of the past 2 months as the evaluation interval for a

question from a questionnaire such as SF-36.

Timing Variables TM-4 Perm --STINT Planned Start of

Assessment

Interval

Char ISO 8601 Timing The start of a planned evaluation or assessment interval

relative to the Time Point Reference

Timing Variables TM-4 Perm --ENINT Planned End of

Assessment

Interval

Char ISO 8601 Timing The end of a planned evaluation or assessment interval

relative to the Time Point Reference


Appendix 1. Table of SDTM Variable Categories and Subcategories

(cross-check each variable before finalizing)

Core Dataset

Structure

Object

Identifier

(OI)

Results

Variables

(RV)

Test

Variable

(TV)

Timing

Variables

(TM)

Mandatory STUDYID ORRES TESTCD VISITDY

Variables DOMAIN STRESC TEST

in Bold SEQ STAT

REASND

EXCLFL

REASEX

OI-1 RV-1 TV-1 TM-1

POOLID SEV CAT DTC

SCAT DY

OI-2 RV-2

USUBJID RESCAT TV-2 TM-2

METHOD TPT

OI-3 RV-3 LLOQ TPTNUM

REFID ORRESU ULOQ ELTM

SPEC STRESN

TPTREF

ANTREG STRESU TV-3 RFTDTC

SPCCND BLFL NAM

SPCUFL EVAL TM3

LAT RV-4

STDTC

DIR ORNRLO

ENDTC

PORTOT ORNRHI

STDY

STNRLO

ENDY

OI-4 STNRHI

DUR

POS STNRC

CSTATE NRIND

TM-4

FAST

EVLINT

STINT

OI-5 ENINT

LOC


Appendix 2. Use Cases for the Custom Domain Resource

Example 1: Mapping micronucleus end-points

A published in vivo mammalian cytogenetics study satisfying the OPPTS 870.5395; OECD 474

guideline was used to model endpoints from an erythrocyte micronucleus assay in mice.

Brief overview of the study (No. 221): Male mice in groups of 6 were administered either test

article, vehicle or positive control (cyclophosphamide). Bone marrow was harvested from the

hind limb (tibia) 24 and 48 hours after dosing. The following endpoints were assessed:

Endpoint Result type Unit

Number of micronucleated erythrocytes per

2000 polychromatic erythrocytes (PCE)

examined per animal

Number (integer) /2000 PCEs/animal

Ratio of polychromatic erythrocytes (PCE) to

monochromatic erythrocytes (NCE)

determined in at least 500 erytrocytes per

animal

Number (float) ratio

Data from the study:

Study day Animal Number # MN PCEs

/2000 PCEs

/animal

Ratio PCE:NCE

24 2602 1 0.47

24 2606 0 0.78

48 2632 2 0.56

The endpoints in the table above are sent through the decision tree, starting from the top left

side. Ideally each of the two endpoints above should be processed through the decision tree

separately; however the outcome through the decision will be the same for both, so only one

run through the decision tree is described below.

The figure below illustrates the steps that this particular data will go through and the

categories of variables selected by answering the questions.



Decision steps:

1. The Core Dataset Structure mandatory variables (STUDYID, DOMAIN, --SEQ) are added

2. There is no need to provide record level references or identifiers, so CD-1 variables are

omitted.

3. The object assessed is not a group of subjects, so the answer to 3 is no.

4. The object assessed is not an entire subject, so the answer to 4 is no.

5. The object assessed is a specimen from a subject (i.e. bone marrow from the hind

limb), so the answer to 5 is yes. Therefore OI-2 (USUBJID), and OI-3 (--REFID, --SPEC,

--ANTREG, --SPCCND, --LAT, --DIR, --PORTOT) variables are added. Note: The answer

to either 3, 4 or 5 must be yes, in this case it was no. 5.

6. The Test mandatory variables (--TESTCD, --TEST) are added.

7. There is no need to further specify the test to distinguish between records, so all other

test variables (TV-1, TV-2 and TV-3) are omitted. The need to further specify a test

could be if the same test was measured using two different methods (i.e. dipstick and

mass spectrometry) or the same test performed by two different labs.

8. The Result mandatory variables (--ORRES, --STRESC, --STAT, --REASND, --EXCLFL, --

REASEX) are added.

9. The results are not character or categorical data, so the answer to 9 is no.

10. The results are numeric (i.e. integer and float), so the answer to 10 is yes. The RV-3

variables (--ORRESU, --STRESN, --STRESU, --BLFL) are added.

11. The results are not categorized for further analysis, so the answer to 11 is no and RV-2

variables are omitted.

12. There are no references ranges provided for the results, so the answer to 12 is no and

RV-4 variables are omitted.

13. The Timing mandatory variable (VISITDY) is added.

14. The test does not have a duration, so the answer to 14 is no. The test is performed at a

single point in time, TM-1 variables (--DTC, --DY) are added.

15. The test is performed relative to a fixed reference (i.e. 24 and 48 hours post dose), so

the answer to 15 is yes and TM-2 variables (--TPT, --TPTNUM, --ELTM, --TPTREF, --

RFTDTC) are added.

The resulting domain structure is given below with all omitted variables removed.


Decision based adding of variables Custom SDTM dataset specification – Micronucleus data

Decision

steps

Variable

category

Variable

group

Core

(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role

Step 1 Core Dataset

structure

Mandatory Req STUDYID Study Identifier Char Identifier

Step 1 Core Dataset

structure


Abbreviation

Char XX Identifier

Step 5 Object Identifier OI-2 Req USUBJID Unique Subject

Identifier

Char Identifier

Step 1 Core Dataset

structure


Number

Num Identifier

Step 5 Object Identifier OI-3 Perm --REFID Reference

Identifier

Char Identifier

Step 6 Test Variables Mandatory Req --TESTCD Measurement,

Test or

Examination

Short Name

Char Controlled

terminology is

expected

Topic

Step 6 Test Variables Mandatory Req --TEST Measurement,

Test or

Examination

Name

Char Controlled

terminology is

expected

Synonym

Qualifier

Step 8 Result Variables Mandatory Exp --ORRES Result or

Finding as

Collected

Char Result

Qualifier

Step 10 Results

Variables

RV-3 Exp --ORRESU Unit of the

Original Result


Qualifier

Step 8 Results

Variables

Mandatory Exp --STRESC Standardized

Result in

Character

Format

Char Controlled

terminology is

expected

Result

Qualifier

Step 10 Results

Variables

RV-3 Exp --STRESN Standardized

Result in

Numeric Format

Num Result

Qualifier

Step 10 Results

Variables

RV-3 Exp --STRESU Unit of the

Standardized

Result


Qualifier

Step 8 Result Variables Mandatory Perm --STAT Completion

Status

Char (ND) Record

Qualifier

Step 8 Result Variables Mandatory Perm --REASND Reason Not

Done

Char Record

Qualifier

Step 5 Object Identifier OI-3 Exp --SPEC Specimen

Material Type

Char (SPEC) Record

Qualifier

Step 5 Object Identifier OI-3 Exp --ANTREG Anatomical

Region of

Specimen

Char Variable

Qualifier

Step 5 Object Identifier OI-3 Perm --SPCCND Specimen

Condition

Char Variable

Qualifier

Step 5 Object Identifier OI-3 Perm --SPCUFL Specimen

Usability for the

Test

Char (NY) Variable

Qualifier

Step 5 Object Identifier OI-3 Perm --LAT Specimen

Laterality within

Subject

Char (LAT) Variable

Qualifier

Step 5 Object Identifier OI-3 Perm --DIR Specimen

Directionality

within Subject

Char (DIR) Variable

Qualifier


Decision based adding of variables Custom SDTM dataset specification – Micronucleus data Decision

steps

Variable

category

Variable

group

Core

(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role

Step 5 Object Identifier OI-3 Perm --PORTOT Portion or

Totality

Char (PORTOT) Variable

Qualifier

Step 10 Result Variables RV-3 Exp --BLFL Baseline Flag Char (NY) Record

Qualifier

Step 8 Results

Variables

Mandatory Perm --EXCLFL Exclusion Flag Char (NY) Record

Qualifier

Step 8 Results Variable Mandatory Perm --REASEX Reason for

Exclusion

Char Record

Qualifier

Step 13 Timing

Variables

Mandatory Exp VISITDY Planned Study

Day

Num Timing

Step 14 Timing

Variables

TM-1 Exp

--DTC Date/Time of

Test

Char ISO 8601 Timing

Step 14 Timing

Variables

TM-1 Exp --DY Study Day of

Test

Num Timing

Step 15 Timing

Variables

TM-2 Exp --TPT Planned Time

Point Name

Char Timing

Step 15 Timing

Variables

TM-2 Exp --TPTNUM Planned Time

Point Number

Num Timing

Step 15 Timing

Variables

TM-2 Exp --ELTM Planned Elapsed

Time from Time

Point Ref


Step 15 Timing

Variables

TM-2 Exp --TPTREF Time Point

Reference

Char Timing

Step 15 Timing

Variables

TM-2 Exp --RFTDTC Date/Time of

Reference Time

Point



The dataset outline based on the domain structure above including example data is shown below. I have decided to name it

“MN” (for Micronucleus), which is populated in the DOMAIN variable and also used as prefix for all variables with -- in their

name in the domain structure.

The permissibility (Core within each variable group) is included. Once the data has been successfully mapped into the dataset

structure and you make sure that you have been able to map all information about each result, then a last exercise to remove

any non-used permissible variables (highlighted in blue) should be performed.

Note that as part of this final step we are removing four mandatory Result Variables because they are permissible and were not

used in the dataset. The expected but un-used variables are still kept in the dataset structure.

The actual date/time information about the results is likely available for data collected in today’s data capture systems, but in

this example that information cannot be populated because of the legacy nature of the used data.

Req Req Req Req Perm Req Req Exp Exp Exp Exp Exp

Row

no.

STUDYID DOMAIN USUBJID MNSEQ MNREFID MNTESTCD MNTEST MNORRES MNORRESU MNSTRESC MNSTRESN MNSTRESU

1 221 MN 221-2602 1 MN_PCE Micronucleated

Polychromatic

Erythrocyte

1 /2000 PCEs

/animal

1 1 /2000 PCEs

/animal

2 221 MN 221-2602 2 PCE/NCE Polychromatic

Monochromatic

Ratio

0.47 Ratio 0.47 0.47 Ratio


Polychromatic

Erythrocyte

0 /2000 PCEs

/animal

0 0 /2000 PCEs

/animal


Monochromatic

Ratio

0.78 Ratio 0.78 0.78 Ratio


Polychromatic

Erythrocyte

2 /2000 PCEs

/animal

2 2 /2000 PCEs

/animal


Monochromatic

Ratio

0.56 Ratio 0.56 0.56 Ratio


(Cont.) Perm Perm Exp Exp Perm Perm Perm Perm Perm Exp Perm Perm

Row no. MNSTAT MNREASND MNSPEC MNANTREG MNSPCCND MNSPCUFL MNLAT MNDIR MNPORTOT MNBLFL MNEXCLFL MNREASEX

1 BONE

MARROW

2 BONE

MARROW

3 BONE

MARROW

4 BONE

MARROW

5 BONE

MARROW

6 BONE

MARROW

(Cont.) Exp Exp Exp Exp Exp Exp Exp Exp

Row no. VISITDY MNDTC MNDY MNTPT MNTPTNUM MNELTM MNTPTREF MNRFTDTC

1 2 2 24 hours after dose 1 P24H Day 1 dose






Reference: http://www.epa.gov/opp00001/chem_search/cleared_reviews/csr_PC-072506_27-Jul-05_a.pdf

http://www.epa.gov/opp00001/chem_search/cleared_reviews/csr_PC-072506_27-Jul-05_a.pdf

Example 2: Mapping Motor Activity

The source of the study data is a mocked study from a live data capture system.

Brief overview of the study (ABC) data:

Individual animals were placed in a cage divided into two boxes with photocells measuring the activity of

the animal based on the crossed photocells in X and Y axis in each box.


Number crossed photocell per axis, time

interval and defined space

Number (integer) count


Study day Animal

Number

Space Time XT YT

5 M1 Box1 5min 862 502

5 M1 Box1 10min 699 465

5 M1 Box1 15min 383 263

5 M1 Box2 5min 484 351

5 M1 Box2 10min 429 259

5 M1 Box2 15min 187 115

Study day 5 was March 10th 2009.

The endpoints in the table above are sent through the decision tree, starting from the top left side. Ideally

each of the two endpoints above should be processed through the decision tree separately; however the

outcome through the decision will be the same for both, so only one run through the decision tree is

described below.

The figure below illustrates the steps that this particular data will go through and the categories of

variables selected by answering the questions.

Decision steps:

1. The Core Dataset Structure mandatory variables (STUDYID, DOMAIN, --SEQ) are added

2. There is no need to provide record level references or identifiers, so CD-1 variables are omitted.

3. The object assessed is not a group of subjects, so the answer to 3 is no.

4. The object assessed is entire subject, so the answer to 4 is yes.

5. The object assessed is not a specimen from a subject (i.e. bone marrow from the hind limb), so

the answer to 5 is no.

6. The assessment is not specific to a location on the animal, so OI-5 variables are omitted.

7. The Test mandatory variables (--TESTCD, --TEST) are added.

8. There is a need to further specify the test to distinguish between records, so the answer to 8 is

yes.

9. The test do not include category, so the answer to 9 is no.

10. The test does include method, so the answer to 10 is yes.

11. The responsability of the test is not important, so the answer to 11 is no.

12. The Result mandatory variables (--ORRES, --STRESC, --STAT, --REASND, --EXCLFL, --REASEX)

are added.

13. The results are not character or categorical data, so the answer to 13 is no (RV-1 and RV-2

variables are omitted).

14. The results are numeric, so the answer to 14 is yes. The RV-3 variables (--ORRESU, --STRESN, --

STRESU, --BLFL) are added.

15. There are no references ranges provided for the results, so the answer to 15 is no and RV-4

variables are omitted.

16. The Timing mandatory variable (VISITDY) is added.

17. The measure have a duration (it is a count per time interval), so the answer to 17 is yes, TM-3

variables (--STDTC, --ENDTC, --STDY, --ENDY, --DUR) are added.

18. The test is performed relative to a fixed reference, so the answer to 18 is yes, TM-2 (--TPT, --

TPTNUM, --ELTM, --TPTREF, --RFTDTC) and TM-4 variables (--EVLINT, --STINT, --ENINT) are

added.

The resulting domain structure is given below with all omitted variables removed.

Decision based adding of variables Custom SDTM dataset specification – Motor Activity data

Decision

steps

Variable

category

Variable

group

Core

(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role

Step 1 Core Dataset

structure


Step 1 Core Dataset

structure


Abbreviation

Char XX Identifier

Step 4 Object

Identifier

OI-2 Req USUBJID Unique Subject

Identifier

Char Identifier

Step 1 Core Dataset

structure


Number

Num Identifier

Step 7 Test Variables Mandatory Req --TESTCD Measurement,

Test or

Examination

Short Name

Char Controlled

terminology is

expected

Topic

Step 7 Test Variables Mandatory Req --TEST Measurement,

Test or

Examination

Name

Char Controlled

terminology is

expected

Synonym

Qualifier

Step 10 Test Variables TV-2 Perm --LOC Location

associated with

a result or

finding

Char Record

Qualifier

Step 10 Test Variables TV-2 Perm --METHOD Method of Test

or Examination

Char Record

Qualifier

Step 12 Result

Variables

Mandatory Exp --ORRES Result or

Finding as

Collected

Char Result

Qualifier

Step 14 Results

Variables

RV-3 Exp --ORRESU Unit of the

Original Result


Qualifier

Step 12 Results

Variables

Mandatory Exp --STRESC Standardized

Result in

Character

Format

Char Controlled

terminology is

expected

Result

Qualifier

Step 14 Results

Variables

RV-3 Exp --STRESN Standardized

Result in

Numeric Format

Num Result

Qualifier

Step 14 Results

Variables

RV-3 Exp --STRESU Unit of the

Standardized

Result


Qualifier

Step 12 Result

Variables

Mandatory Perm --STAT Completion

Status

Char (ND) Record

Qualifier

Step 12 Result

Variables

Mandatory Perm --REASND Reason Not

Done

Char Record

Qualifier

Step 14 Result

Variables

RV-3 Exp --BLFL Baseline Flag Char (NY) Record

Qualifier

Step 12 Results

Variables

Mandatory Perm --EXCLFL Exclusion Flag Char (NY) Record

Qualifier

Step 12 Results

Variable

Mandatory Perm --REASEX Reason for

Exclusion

Char Record

Qualifier

Step 16 Timing

Variables

Mandatory Exp VISITDY Planned Study

Day

Num Timing

Step 17 Timing

Variables

TM-3 Exp --STDTC Start Date/Time

of Test


Step 17 Timing

Variables

TM-3 Perm --ENDTC End Date/Time

of Test


Decision based adding of variables Custom SDTM dataset specification – Motor Activity data

Decision

steps

Variable

category

Variable

group

Core

(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role

Step 17 Timing

Variables

TM-3 Exp --STDY Study Day of

Start of Test

Num Timing

Step 17 Timing

Variables

TM-3 Perm --ENDY Study Day of

End of Test

Num Timing

Step 17 Timing

Variables

TM-3 Perm --DUR Duration of Test Char ISO 8601 Timing

Step 18 Timing

Variables

TM-2 Exp --TPT Planned Time

Point Name

Char Timing

Step 18 Timing

Variables

TM-2 Exp --TPTNUM Planned Time

Point Number

Num Timing

Step 18 Timing

Variables

TM-2 Exp --ELTM Planned Elapsed

Time from Time

Point Ref


Step 18 Timing

Variables

TM-2 Exp --TPTREF Time Point

Reference

Char Timing

Step 18 Timing

Variables

TM-2 Exp --RFTDTC Date/Time of

Reference Time

Point


Step 18 Timing

Variables

TM-4 Perm --EVLINT Evaluation

Interval


Step 18 Timing

Variables

TM-4 Perm --STINT Planned Start of

Assessment

Interval


Step 18 Timing

Variables

TM-4 Perm --ENINT Planned End of

Assessment

Interval


The dataset outline based on the domain structure above including example data is shown below. I have decided to name it “MC”

(for Motor Activity - MA is already used), which is populated in the DOMAIN variable and also used as prefix for all variables with --

in their name in the domain structure.

The results were collected over a planned collection interval of 5 minutes each, which is reflected in the ISO8601 duration format in

MCEVLINT (PT5M). Each time point described in TPT is labelled with the end of the interval, and the planned start and end of the

collection interval is represented in MCSTINT and MCENINT, respectively.

Any permissible variables not used to model the data (indicated in red) can be omitted from the dataset.

Req Req Req Req Req Req Exp Exp Exp Exp Exp

Row

no. STUDYID DOMAIN USUBJID MCSEQ MCTESTCD MCTEST MCORRES MCORRESU MCSTRESC MCSTRESN MCSTRESU

1 ABC MC ABC-M1 1 MC_XT Motor Activity Cross X Line 862 count 862 862 count 2 ABC MC ABC-M1 2 MC_YT Motor Activity Cross Y Line 502 count 502 502 count 3 ABC MC ABC-M1 3 MC_XT Motor Activity Cross X Line 699 count 699 699 count 4 ABC MC ABC-M1 4 MC_YT Motor Activity Cross Y Line 465 count 465 465 count 5 ABC MC ABC-M1 5 MC_XT Motor Activity Cross X Line 383 count 383 383 count 6 ABC MC ABC-M1 6 MC_YT Motor Activity Cross Y Line 263 count 263 263 count 7 ABC MC ABC-M1 7 MC_XT Motor Activity Cross X Line 484 count 484 484 count 8 ABC MC ABC-M1 8 MC_YT Motor Activity Cross Y Line 351 count 351 351 count 9 ABC MC ABC-M1 9 MC_XT Motor Activity Cross X Line 429 count 429 429 count

10 ABC MC ABC-M1 10 MC_YT Motor Activity Cross Y Line 259 count 259 259 count 11 ABC MC ABC-M1 11 MC_XT Motor Activity Cross X Line 187 count 187 187 count 12 ABC MC ABC-M1 12 MC_YT Motor Activity Cross Y Line 115 count 115 115 count

(Cont.) Perm Perm Perm Exp Perm Perm

Row no. MCMETHOD MCSTAT MCREASND MCBLFL MCEXCLFL MCREASEX 1 Box1 2 Box1 3 Box1 4 Box1 5 Box1 6 Box1 7 Box2 8 Box2 9 Box2

10 Box2 11 Box2 12 Box2

(Cont.) Exp Exp Perm Exp Perm Perm Exp Exp Exp Exp Exp Row no. VISITDY MCSTDTC MDENDTC MCSTDY MCENDY MCDUR MCTPT MCTPTNUM MCELTM MCTPTREF MCRFTDTC 1 5 2009-03-10 2009-03-10 5 5 PT5M 5 minutes after dose 1 Day 5 dose 2009-03-10

2 5 2009-03-10 2009-03-10 5 5 PT5M 5 minutes after dose 1 Day 5 dose 2009-03-10











(Cont.) Perm Perm Perm

Row no. MCEVLINT MCSTINT MCENINT 1 PT5M PT0M PT5M

2 PT5M PT0M PT5M

3 PT5M PT5M PT10M

4 PT5M PT5M PT10M

5 PT5M PT10M PT15M

6 PT5M PT10M PT15M

7 PT5M PT0M PT5M

8 PT5M PT0M PT5M

9 PT5M PT5M PT10M

10 PT5M PT5M PT10M

11 PT5M PT10M PT15M

12 PT5M PT10M PT15M

Example 3: Ocular Irritation

Study Number: 8289B

Title: “Primary Eye Irritation Study of Alipal CO-436 in New Zealand White Rabbits”

Study Date: 9/24/84

Accessed at: http://www.epa.gov/oppt/tsca8e/pubs/8ehq/2011/apr11/8ehq-0411-01708b.pdf

Summary:

New Zealand White Rabbits each received a single ocular dose of 0.1 mL of Alipal CO-436 with either no

washout (n=6) or a 30-second washout (n=3) with physiological saline. After administration of the test

article, the eyes were examined at 24, 48, and 72 hours, then at 7, 10, 13, 16, 19 and 21 days. For each

animal, the cornea, iris and conjunctiva were scored for irritation. The test article was administered to

one eye for each animal, with the second eye serving as an untreated control. Irritation was scored on a

classification system (i.e. Draize Scale) where numeric values are used to describe the level of irritation

(Appendix I). The sponsor recorded ocular irritation for each individual animal and then presented group

means for “no washout group” and “30-second washout group” at each time point.


Draize scoring (various tissues) Number (integer) N/A (rank)

Draize totals (derived values) Number (integer) N/A


Animal

Number

Draize scoring Time

Tissue assessment 24 h 48 h 72 h Day 7 Day 10 84-3240 A - Cornea Opacity 1 1 1 1 1

B - Cornea Area Involved 4 4 2 1 1 Dose: 0.1 mL C - Iris 1 1 1 1 1

D - Conjuctiva redness 2 3 2 2 2 Rinse 30 sec E - Conjuctive Chemosis 3 3 4 3 3

After F - Conjuctiva Discharge 3 3 2 3 2 1 - Cornea Total ((A+B) x 5) 20 20 10 5 5 2 - Iris Total (C x 5) 5 5 5 5 5 3 - Conjuctivae Total ((D+E+F) x 2) 16 18 16 16 14 Total (1+2+3) 41 43 31 26 24

84-3240 A - Cornea Opacity 0 0 0 0 0 B - Cornea Area Involved 0 0 0 0 0

Dose: N/A C - Iris 0 0 0 0 0 Untreated D - Conjuctiva redness 0 0 0 0 0

eye E - Conjuctive Chemosis 0 0 0 0 0 F - Conjuctiva Discharge 0 0 0 0 0 1 - Cornea Total ((A+B) x 5) 0 0 0 0 0 2 - Iris Total (C x 5) 0 0 0 0 0 3 - Conjuctivae Total ((D+E+F) x 2) 0 0 0 0 0 Total (1+2+3) 0 0 0 0 0

The data highlighted in green is the data that is modelled as an example dataset.

The endpoints in the table above are sent through the decision tree, starting from the top left side. Ideally

each of the two endpoints above should be processed through the decision tree separately; however the

outcome through the decision will be the same for both as they are both integers without units, so only

one run through the decision tree is described below.

The figure below illustrates the steps that this particular data will go through and the categories of

variables selected by answering the questions.

http://www.epa.gov/oppt/tsca8e/pubs/8ehq/2011/apr11/8ehq-0411-01708b.pdf

Decision steps:

Step 1. Add Mandatory variable from Core Dataset Structure (STUDYID, DOMAIN, --SEQ).

Step 2. Reference level identifiers will not be added, so the answer is “No” to the question in the

Core Domain structure. Variables in CD-1 will not be added.

Step 3. The object being assessed is not a group of subjects (“No”), so the OI-2 variables are added

(USUBJID)

Step 4. The object beings assessed is an intact (entire) subject (“Yes”), because no specimen have

been excised from the subject.

Step 5. The state of the subject is not important for the interpretation of the result (“No”), so OI-4

variables are not added.

Step 6. The test is specific to a location on the intact subject (it is an eye assessment). The answer

is “Yes”, so OI-5 variables are added (--LOC).

Step 7. Add Mandatory variables for “Test” lane (--TESTCD, --TEST)

Step 8. There is no need to further specify the test to distinguish records (“No”), so the TV-1, TV-2

and TV-3 variables are omitted. Though it is tempting to think of “rinse” vs . “No-rinse” as a

methjod, it is more appropriate to place this aspect of the treatment in the EX (Exposure)

Domain (see the SEND Implementation Guide for further information).

Step 9. Add Mandatory variables for “Results” lane (--ORRES, --STRESC, --STAT, --REASND, --

EXCLFL, --REASEX).

Step 10. The results are not character format or categories (“No”).

Step 11. The results are quantitative (numerical scoring), so RV-3 variables are added (--ORRESU, --

STRESN, --STRESU, --BLFL).

Step 12. There are no reference ranges for numerical scoring. RV-4 variables are not added.

Step 13. Add Mandatory Timing Variables (VISITDY).

Step 14. The individual measurement does not have a duration (i.e. “No”). Because it is a

measurement taken at several single points in time, TM-1 variables are added (--DTC, --

DY).

Step 15. The individual measurement is planned relative to a fixed reference (“Yes”), so we add

relevant variables from TM-2 (--TPT, --TPTNUM, --ELTM, --TPTREF, --RFTDTC).

Finally all variables must be sorted so that they are in the same sequence as the Domain Table. The

resulting ocular Irritation domain structure is given below.

Decision based adding of variables Custom SDTM dataset specification – Ocular Irritation data

Decision

Steps

Variable category Variable

group

Core

(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role

Step 1 Core Dataset

structure


Step 1 Core Dataset

structure


Abbreviation

Char XX Identifier

Step 3 Object Identifier OI-2 Req USUBJID Unique Subject

Identifier

Char Identifier

Step 1 Core Dataset

structure

Mandatory Req --SEQ Sequence Number Num Identifier

Step 7 Test Variables Mandatory Req --TESTCD Measurement, Test

or Examination

Short Name

Char Controlled

terminology

is expected

Topic

Step 7 Test Variables Mandatory Req --TEST Measurement, Test

or Examination

Name

Char Controlled

terminology

is expected

Synonym

Qualifier

Step 9 Result Variables Mandatory Exp --ORRES Result or Finding as

Collected

Char Result

Qualifier

Step 11 Results Variables RV-3 Exp --ORRESU Unit of the Original

Result


Qualifier

Step 9 Results Variables Mandatory Exp --STRESC Standardized Result

in Character Format

Char Controlled

terminology

is expected

Result

Qualifier

Step 11 Results Variables RV-3 Exp --STRESN Standardized Result

in Numeric Format

Num Result

Qualifier

Step 11 Results Variables RV-3 Exp --STRESU Unit of the

Standardized Result


Qualifier

Step 9 Result Variables Mandatory Perm --STAT Completion Status Char (ND) Record

Qualifier

Step 9 Result Variables Mandatory Perm --REASND Reason Not Done Char Record

Qualifier

Step 6 Object Identifier OI-5 Perm --LOC Location associated

with a result or

finding

Char Record

Qualifier

Step 11 Result Variables RV-3 Exp --BLFL Baseline Flag Char (NY) Record

Qualifier

Step 9 Results Variables Mandatory Perm --EXCLFL Exclusion Flag Char (NY) Record

Qualifier

Step 9 Results Variable Mandatory Perm --REASEX Reason for

Exclusion

Char Record

Qualifier

Step 13 Timing Variables Mandatory Exp VISITDY Planned Study Day Num Timing

Step 14 Timing Variables TM-1 Exp

--DTC Date/Time of Test Char ISO 8601 Timing

Step 14 Timing Variables TM-1 Exp --DY Study Day of Test Num Timing

Decision based adding of variables Custom SDTM dataset specification – Ocular Irritation data

Decision

Steps

Variable category Variable

group

Core

(within

variable

group)

Variable

Name


Terms,

Codelist, or

Format

Role

Step 15 Timing Variables TM-2 Exp --TPT Planned Time Point

Name

Char Timing

Step 15 Timing Variables TM-2 Exp --TPTNUM Planned Time Point

Number

Num Timing

Step 15 Timing Variables TM-2 Exp --ELTM Planned Elapsed

Time from Time

Point Ref


Step 15 Timing Variables TM-2 Exp --TPTREF Time Point

Reference

Char Timing

Step 15 Timing Variables TM-2 Exp --RFTDTC Date/Time of

Reference Time

Point


The dataset outline based on the domain structure above including example data is shown below. I have decided to name it “OC”

(for Ocular Irritation), which is populated in the DOMAIN variable and also used as prefix for all variables with -- in their name in the

domain structure.

The results are numeric, but they are a ranking, so the unit variables (OCORRESU and OCSTRESU) are not used for this data, but

they are left in the dataset as they are both Expected.

Typically the report would reflect which eye that was administered test article and which that was not (left and right). However this

data unless indicate that it was one and the other, so the location of the observation (indicated in OCLOC) is equally unspecific (Eye,

treated and Eye, untreated).

The data that is used in the example below is from 24 hours after test article administration; therefore the planned study day of

assessment is study day 2.

Dosing occurred on November 9th 1984 according to the report, so we can populate the date/time variables (OCDTC and OCRFTDTC)

based on this information.

For this study the following tests and test codes could be

--TESTCD* --TEST*

DSCOOP Draize Score: Cornea Opacity

DSCOAR Draize Score: Cornea Area Involved

DSI Draize Score: Iris

DCCOJRD Draize Score: Conjuctiva redness

DSCOJCM Draize Score: Conjuctive Chemosis

DSCOJDC Draize Score: Conjuctiva Discharge

DSCOTOT Draize Score: Cornea Total

DSITOT Draize Score: Iris Total

DSCOJTOT Draize Score: Conjuctivae Total

DSTOT Driaze Score: Total

*Note: These codes are not published controlled terminology.

Any permissible variables not used to model the data (indicated in red) can be omitted from the dataset.

Req Req Req Req Req Req Exp Exp Exp Exp Exp

Row

no. STUDYID DOMAIN USUBJID OCSEQ OCTESTCD OCTEST OCORRES OCORRESU OCSTRESC OCSTRESN OCSTRESU

1 8289B OC 8289B-

843240

1 DSCOOP Draize Score: Cornea Opacity 1 1 1

2 8289B OC 8289B-

843240

2 DSCOAR Draize Score: Cornea Area

Involved 4 4 4

3 8289B OC 8289B-

843240

3 DSI Draize Score: Iris 1 1 1

4 8289B OC 8289B-

843240

4 DCCOJRD Draize Score: Conjuctiva redness 2 2 2

5 8289B OC 8289B-

843240

5 DSCOJCM Draize Score: Conjuctive Chemosis 3 3 3

6 8289B OC 8289B-843240

6 DSCOJDC Draize Score: Conjuctiva Discharge 3 3 3

7 8289B OC 8289B-

843240

7 DSCOTOT Draize Score: Cornea Total 20 20 20

8 8289B OC 8289B-843240

8 DSITOT Draize Score: Iris Total 5 5 5

9 8289B OC 8289B-

843240

9 DSCOJTOT Draize Score: Conjuctivae Total 16 16 16

10 8289B OC 8289B-843240

10 DSTOT Driaze Score: Total 41 41 41

11 8289B OC 8289B-

843240

11 DSCOOP Draize Score: Cornea Opacity 0 0 0

12 8289B OC 8289B-843240

12 DSCOAR Draize Score: Cornea Area Involved

0 0 0

(Cont.) Perm Perm Perm Exp Perm Perm

Row no. OCSTAT OCREASND OCLOC OCBLFL OCEXCLFL OCREASEX 1 Eye, Treated 2 Eye, Treated 3 Eye, Treated 4 Eye, Treated 5 Eye, Treated 6 Eye, Treated 7 Eye, Treated 8 Eye, Treated 9 Eye, Treated

10 Eye, Treated 11 Eye, Untreated 12 Eye, Untreated

(Cont.) Exp Exp Exp Exp Exp Exp Exp Exp

Row no. VISITDY OCDTC OCDY OCTPT OCTPTNUM OCELTM OCTPTREF OCRFTDTC

1 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03





6 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03 7 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03 8 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03 9 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03 10 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03 11 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03 12 2 1984-09-04 2 24 hours after dose 1 PT24H Dosing of eye 1984-09-03

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