Controlled Terminology Mapping/Alignment Across Codelists Slides_1.pdf · • including domain specific variables and test level responses. •Mapping based upon SDTM 1.4, SDTMIG

Controlled Terminology Mapping/Alignment Across Codelists

Presented by Donna Sattler, Erin Muhlbradt, Ph.D., and Anthony Chow

8 Jan 2019

Panelists

• Donna Sattler, Consultant, Data Standards, J&J

• Erin Muhlbradt, PhD., Clinical/Biomedical Information Specialist at MSC

• Anthony Chow, Director of SHARE, CDISC

Housekeeping

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• A short marketing presentation on upcoming CDISC learning opportunities will follow Q&A portion; will answer additional incoming questions that come in

Submitting Questions

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• General: ‘Question’

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Content Disclaimer

The purpose of this webinar is to provide examples of implementation and should not be considered official recommendations by the standards development teams or CDISC unless otherwise stated in the presentation.

This webinar is not considered to be an authorized CDISC course, is not developed or delivered under CDISC procedures, and should not replace a published CDISC IG or UG. Please refer to the latest published standards documents for the most authoritative implementation information.

Controlled TerminologyMapping & Alignment Across Codelists

Presented by Donna Sattler, Erin Muhlbradt, and Anthony Chow

2019-01-08

Disclaimer

All materials in this presentation are for illustration purposes and do not constitute final product. Tables and figures are often cropped for brevity.

Agenda

1. Introduction

2. Programmers Practicum

3. Implementation Challenges

4. Next Steps

Introduction

CDISC Controlled Terminology

• … is the set of codelists and valid values used with data items within CDISC-defined datasets.

• … provides submission values, definitions, codelists, and c-codes for all terms.

• … provides the values required for submission to FDA and PMDA in CDISC-compliant datasets.

• … does not tell you WHAT to collect; it tells you IF you collected a particular data item, how to submit it in your electronic dataset.

1/14/2019CDISC Webinar 10

CDISC Controlled Terminology


• Consists of questions (e.g., Variables, TEST/CDs, and PARM/CDs)

• Consists of answers (e.g., response codelists, qualifier variable codelists, etc.)

• All terms are bundled together into codelists, which are published alphabetically in the Controlled Terminology publications.

Initial Problem Statement:

“Relationships between published codelists and metadata are not explicit

enough or are incomplete in published IGs and TAUGs.”


… Turned into several Problem Statements

The use case of Controlled Terminology has

matured from simple “one variable,

one codelist.” Conditional codelists,

value subsets, and other new

scenarios are becoming prevalent in

various CDISC products. We need to provide

implementers information how to apply these

new scenarios when they implement our

standards.

Industry feedback tells us codetables

posted on CDISC are very useful to

jumpstart implementation. But to

improve consistency and increase

production; we need some kind of

formalism, such as value-level

metadata.


Publication frequency of Controlled

Terminology outpaces

Implementation Guides and User

Guides. This creates a late binding

effect where new codelists are created

(or, codelists renamed and deprecated)

post-publication. It is time to re-

evaluate our current process and tackle

this historical problem.

Lastly, new information cannot be effectively managed and maintained in [two-dimensional] spreadsheets. Rich metadata is needed to properly express their intricacies.

Multi-Dimensional View of CT


Common Programming Dilemma

Which Variables

are subject to

controlled

terminology?


Programming CT Tools:

There are 683 CT values for

UNIT. What is appropriate for

Con Meds?


Mapping Rules and Instructions

https://www.pha

rmasug.org/pro

ceedings/2017/I

B/PharmaSUG-

2017-IB05.pdf


Implementation Challenges

Implementation Challenge #1: How do I know which codelist to use for this variable?

• In fact, there are over 860 codelists published to date (as of 2018-12-21), of which 759 of them are present in the SDTM terminology publication.

• How does one know which codelist to use for which model element?

• The Implementation Guides gives some information (but it becomes out of date quickly)

• The codelist names may provide some clues (but not always apparent in all)

• What/where is the definitive source that explicitly states which codelist belongs to which variable?


What does the industry need from CDISC to help implement CDISC CT?

1. Defined a project scope

2. Put a team together

3. Identified Deliverables


This Photo by Unknown

Author is licensed under

CC BY

https://wiki.cdisc.org/display/CT/CT+Relati

onships+Sub+Team

http://www.ventilab.org/2012/11/25/avviso-flow-limitation-nei-pazienti-in-ventilazione-meccanica-progetto-di-studio-collaborativo/#comments

https://creativecommons.org/licenses/by/3.0/


CT Relationships Team Scope:

Deliverable Description

Identify Usage

Scenarios

Simple Codelist, Conditional Codelist, Multiple

Codelist, TAUG Specific Codelist, CT for

(NSV)/ SUPPQUAL, Codelist Supersets &

Subsets, Define.xml, Codetable-ese details

Codelist to Metadata

Mapping File

SHARE export of baseline metadata. Team

crosschecked content with 3.2 IG and

SDTM1.4. Identified gaps and needs as well

as issues. New Metadata Display and

Codetable conversion emerged.

CT Policy

Recommendations

These will be logged for use by the Controlled

Terminology Implementation Guide team.

Codelist Subsets &

Supersets

Relationships

Still in concept Phase: Instead of publishing

multiple packages (ADaM, SDTM, SEND,

CDASH), publish 1 big dictionary and tag

codelist and/or terms with usage.

The Fix: Codelist to Variable Mapping File

• The mapping will explicitly define the relationship between published codelists and the elements within the CDISC model.

• including domain specific variables and test level responses.

• Mapping based upon SDTM 1.4, SDTMIG 3.2

• Will include specific regulatory requirements based on published technical conformance guide and data standards catalog (FDA and PMDA).

• The mapping development is being overseen by the CT Relationships team.

• The team has reviewed one domain from each observation class (Events=AE; Interventions=CM; Findings=LB) and a special purpose domain (TS).



Building the model

What will this mean to SHARE?


Simple one-to-one scenario

OID Domain Variable CDISC CT Codelist Short Name CDISC CT Codelist C-Code CDISC CT Codelist Long Name

AE.AESEV AE AESEV AESEV C66769

Severity/Intensity Scale for

Adverse Events

AE.AEACN AE AEACN ACN C66767

Action Taken with Study

Treatment


Simple one-to-one scenario

For Use


Subset value list from codelist


Subset value list from codelist

OID Domain Variable CDISC CT Codelist Short Name CDISC CT Codelist C-Code CDISC CT Codelist Long Name Permissible Values from CDISC CT

AE.AEPRESP AE AEPRESP NY C66742 No Yes Response Y (C49488)

AE.AEENRTPT AE AEENRTPT STENRF C66728 Relation to Reference Period

AFTER (C38008); BEFORE (C25629);

COINCIDENT (C25456); ONGOING

(C53279); UNKNOWN (C17998)

For Use But Only


External codelist to a specific element


External codelist to a specific element

OID Domain Variable External Dictionary's Organization External Dictionary's Name External Dictionary's Component

AE.AEPTCD AE AEPTCD MSSO MedDRA Preferred Term Code

AE.AEHLGT AE AEHLGT MSSO MedDRA High Level Group Term

For Use


Non-specific external codelist requirement


Non-specific external codelist requirement

OID Domain Variable Controlled Terminology Description

AE.AEBODSYS AE AEBODSYS

System organ class from the coding dictionary associated with the adverse event by the

sponsor, e.g., MedDRA

For Use


With condition and context


With condition and context

OID Domain Variable Condition

CDISC CT Codelist

Short Name

CDISC CT Codelist

C-Code

CDISC CT Codelist Long

Name Tagged Usage

SUPPCM.QVAL.OUTTRT SUPPCM QVAL QNAM EQ "OUTTRT" AVOUTTRT C120521

Anti-Viral Outcome of

Treatment TAUG-Chronic Hepatitis C v1.0

SUPPCM.QVAL.EVDRETRT SUPPCM QVAL QNAM EQ "EVDRETRT" EVDRETRT C102579

Supporting Evidence for

Re-Treatment TAUG-Tuberculosis v2.0

SUPPCM.QVAL.REASTRT SUPPCM QVAL QNAM EQ "REASTRT" REASTRT C102584 Reason For Treatment TAUG-Tuberculosis v2.0

SUPPCM.QVAL.TRTINT SUPPCM QVAL QNAM EQ "TRTINT" TRTINTNT C124307 Treatment Intent TAUG-Breast Cancer v1.0

SUPPCM.QVAL.TRTSTT SUPPCM QVAL QNAM EQ "TRTSTT" TRTSET C124308 Treatment Setting TAUG-Breast Cancer v1.0

SUPPCM.QVAL.VCNEVD SUPPCM QVAL QNAM EQ "VCNEVD" VCNEVD C102590

Vaccination Evidence

Source TAUG-Tuberculosis v2.0

SUPPAE.QVAL.AETRTEM SUPPAE QVAL QNAM EQ "AETRTEM" NY C66742 No Yes Response

For Where Use When


Putting them back together in a model


Putting them back together in a model

# Metadata element

1 OID

2 Domain

3 Variable

4 Constraint

5 Usage

6 CDISC CT Codelist Short Name

7 CDISC CT Codelist C-Code

8 CDISC CT Codelist Long Name

9 Permissible Values from CDISC CT

10 External Dictionary's Organization

11 External Dictionary's Name

12 External Dictionary's Component

13 Controlled Terminology Description

Lessons learned and considerations:

• The IG and model need to be used together to get a nearly complete picture.

• There is a grey area about those variables that we suspect would not be used 99.99% of the time.

• The variables present in the IG are only the variables that are REQUIRED and EXPECTED and sometimes PERMISSABLE to be present in the domain. There are several other variables that can be utilized to accommodate your study design.

• Regulatory requirements will need to be taken into consideration; there is more than one regulator on the block!

• How do we handle versioning? Model version, IG version, CT version, etc.

• From the programmer’s perspective, they need to know what CT values are appropriate per:

• CRF Form / Domain Level

• Variable / Codelist Relationships

• Codelist Subsets pertinent per Domain like UNIT for CM and VS


Implementation Challenge #2: How do I pair TEST and TESTCD or PARM and PARMCD?

• The current configuration of the published terminology has that there are two codelists for a test or parameter; one containing the 40 character (or less) long name and one containing the 8 character (or less) short name.

• The NCI c-code in column A can be used to find the paired submission values for the long and short name of the term, since the concept code is identical across both codelists.

• The synonym column always contains the long name but may also contain additional synonyms.

• Not directly electronically consumable in the current state.


C-code

(Concept

Code)

Urinary System Test

Code

(URNSTSCD)

(codelist code =

C129942)

Urinary System Test Name

(URNSTS)

(codelist code = C129941)

C64546 COLOR Color

C135522 GRFTSTAT Graft Status

C25334 LENGTH Length

C130195 RNLANUM Number of Renal Arteries

C130196 RNLVNUM Number of Renal Veins

C-code

(Concept

Code)

Microbiology

Susceptibility Test Code

(MSTESTCD)

(codelist code =

C128688)

Microbiology Susceptibility Test Name

(MSTEST)


C147471 DIAZOINH Diameter of the Zone of Inhibition

C116255 ICNETAS Inhibitory Concentration Net Assessment

C139114 MEC50FCB Microbial EC50 Fold Change from

Baseline

C139115 MEC50FCR Microbial EC50 Fold Change from Ref

C139116 MEC50R Microbial EC50 Reference Control Result

C139117 MEC50S Microbial EC50 Subject Result

C128985 MIC Minimum Inhibitory Concentration

C139118 MIC50FCB Microbial IC50 Fold Change from Baseline

C139119 MIC50FCR Microbial IC50 Fold Change from Ref

C139120 MIC50R Microbial IC50 Reference Control Result

C139121 MIC50S Microbial IC50 Subject Result

C139122 MIC95FCB Microbial IC95 Fold Change from Baseline

C139123 MIC95FCR Microbial IC95 Fold Change from Ref

C139124 MIC95R Microbial IC95 Reference Control Result

C139125 MIC95S Microbial IC95 Subject Result

C85540 MICROSUS Microbial Susceptibility

C-code

(Concept

Code)

Oncology Response

Assessment Test Code

(ONCRTSCD)


Oncology Response Assessment Test

Name

(ONCRTS)


C94536 BESTRESP Best Overall Response

C135477 BMIVLIND Bone Marrow Involvement Indicator

C132455 BONERESP Bone Response

C123619 CLINRESP Clinical Response

C135478 CPRFSTAT Clinical Performance Status

C123620 CYTORESP Cytogenetic Response

C123621 DRCRIND Disease Recurrence Indicator

C123622 HEMARESP Hematologic Response

C135479 LIVRRESP Liver Response

C123623 METBRESP Metabolic Response

C132456 METSIND Metastatic Indicator

C123624 MOLRESP Molecular Response

C124433 MRDRESP Minimal Residual Disease Response

C123625 MRPHRESP Morphologic Response

C142362 NEWLIND New Lesion Indicator

C103420 NEWLPROG New Lesion Progression

C142363 NEWLWIND New Lesion Worsening Indicator

C135480 NTERESP Non-Target Enhancing Response

C142364 NTLWIND Non-Target Lesion Worsening Indicator

C135481 NTNERESP Non-Target Non-Enhancing Response

C94535 NTRGRESP Non-target Response

C96613 OVRLRESP Overall Response

C123626 PATHRESP Pathologic Response

C123627 RDIORESP Radiologic Response

C132457 SFTSRESP Soft Tissue Response

C135482 SPLNRESP Spleen Response

C135483 STRUSTAT Steroid Use Status

C124434 SYMPTDTR Symptomatic Deterioration

C132458 TMRESP Tumor Marker Response

C94534 TRGRESP Target Response

The Fix: An alternative view of TEST/CD and PARM/CD codelists programmatically generated each quarter.

C-code

(Concept

Code)

Biospecimen

Characteristics Test

Code

(BSTESTCD)

(codelist code =

C124300)

Biospecimen Characteristics Test Name

(BSTEST)


C139281 A260A230 A260/A230 Ratio

C139280 A260A280 A260/A280 Ratio

C25244 AREA Area

C41185 CONC Concentration

C128948 FIXNAM Fixative Name

C139282 FLUORLBL Fluorescent Label

C25334 LENGTH Length

C43246 MASS Mass

C25283 QUALITY Quality

C63637 RIN RNA Integrity Number

C25681 SIZE Size

C106569 SPWEIGHT Specimen Weight

C25206 TEMP Temperature

C41145 THICK Thickness

C135371 TUMTORI Tumor Tissue Origin

C139279 VBLSIND Sample Viability Indicator

C139278 VBLSPCT Sample Viability Percent

C25335 VOLUME Volume

C25345 WIDTH Width

C-code

(Concept

Code)

Device Identifier Short

Name (DIPARMCD)

(codelist code =

C106481)

Device Identifier Long Name

(DIPARM)


C104504 BATCH Batch Number

C106570 SFMTYP Stereotactic Surgery Frame Type

C111191 SECURLD Secure Lead Type

C112279 FDAUDI FDA Unique Device Identification

C25392 MANUF Manufacturer

C53265 DEVTYPE Device Type

C70848 LOT Lot Number

C71898 TRADENAM Trade Name

C73518 SERIAL Serial Number

C99285 MODEL Model Number

C99286 CATNUM Catalog Number

C-code

(Concept

Code)

Holter ECG Test Code

(HETESTCD)

(codelist code =

C120523)

Holter ECG Test Name

(HETEST)


C111131 AVCOND Atrioventricular Conduction

C111132 AXISVOLT Axis and Voltage

C111155 CHYPTENL Chamber Hypertrophy or Enlargement

C117761 EGCOMP Comparison to a Prior ECG

C41255 INTP Interpretation

C111238 IVTIACD Intraventricular-Intraatrial Conduction

C111280 MI Myocardial Infarction

C111285 PACEMAKR Pacemaker

C111307 RHYNOS Rhythm Not Otherwise Specified

C111312 SNRARRY Sinus Node Rhythms and Arrhythmias

C111320 SPRARRY Supraventricular Arrhythmias

C111321 SPRTARRY Supraventricular Tachyarrhythmias

C111363 STSTWUW ST Segment, T wave, and U wave

C117807 TECHQUAL Technical Quality

C111330 VTARRY Ventricular Arrhythmias

C111331 VTTARRY Ventricular Tachyarrhythmias

C-code

(Concept

Code)

Drug Accountability Test

Code

(DATESTCD)


Drug Accountability Test Name

(DATEST)


C78721 DISPAMT Dispensed Amount

C78722 RETAMT Returned Amount

C-code

(Concept

Code)

SDTM Death Diagnosis

and Details Test Code

(DTHDXCD)

(codelist code =

C116108)

SDTM Death Diagnosis and Details Test

Name

(DTHDX)


C135383 AGEDTH Age at Death

C135384 AUTOPIND Autopsy Indicator

C135385 DTHCOIND Death Certificate Obtained Indicator

C135386 HMROIND Hospital Medical Record Obtained Ind

C124331 LOCDTH Location of Death

C99531 PRCDTH Primary Cause of Death

C116142 SECDTH Secondary Cause of Death

C-code

(Concept

Code)

Subject Status Test

Code

(SSTESTCD)

(codelist code =

C112024)

Subject Status Test Name

(SSTEST)


C25717 SURVSTAT Survival Status

C-code

(Concept

Code)

Tumor or Lesion

Identification Test Code

(TUTESTCD)


Tumor or Lesion Identification Test

Name

(TUTEST)


C123633 DRCRLTLC Disease Recurrence Relative Location

C119567 GRLIDENT Graft Lesion Identification

C94189 LESIDENT Lesion Identification

C119568 LMLIDENT Limb Lesion Identification

C154853 METIND Metastatic Tumor Site Indicator

C94525 TUMERGE Tumor Merged

C94523 TUMIDENT Tumor Identification

C96642 TUSPLIT Tumor Split

C119569 VSLIDENT Vessel Lesion Identification

C-code

(Concept

Code)

Device Properties Test

Code (DOTESTCD)

(codelist code =

C111111)

Device Properties Test Name

(DOTEST)


C53414 COMPOS Composition

C142234 DIGSMPRT Digital Sampling Rate

C154712 DINTMKNM Dinucleotide Marker Names

C142235 ECSNRTYP Electrical Current Sensor Type

C112278 FDADEVCL FDA Device Classification

C41184 INDC Indication for Use

C154711 IORFAREA Internal Orifice Area

C120606 LUMNCTYP Luminescence Type

C150830 MONTMKNM Mononucleotide Marker Names

C116119 MRICTYPE MRI Coil Type

C116118 MULTPLEX Multiplex Probe Parameter

C150831 PENTMKNM Pentanucleotide Marker Names

C112332 PORESIZE Pore Size

C112406 REAGLOT Reagent Lot

C116120 SCRYSTYP Scintillation Crystal Type

C150832 SFTWRNAM Software Name

C111093 SFTWRVER Software Version

C70855 SHLFLIFE Shelf Life

C25681 SIZE Size

C112421 SRGMSHOA Surgical Mesh Open Area


C41145 THICKNSS Thickness

C-code

(Concept

Code)

Gastrointestinal Test

Code

(GASTROCD)

(codelist code =

C128682)

Gastrointestinal Test Name

(GASTRO)


C119332 ELASTIC Elasticity

C139184 RTAVDIST Rectal Tumor to Anal Verge Distance

C-code

(Concept

Code)

Nervous System

Findings Test Code

(NVTESTCD)

(codelist code =

C116104)

Nervous System Findings Test Name

(NVTEST)


C114183 BSI Boundary Shift Integral

C154865 CRBBLFLW Cerebral Blood Flow

C117886 N145LAT N145 Latency

C154868 N1SLPDUR N1 Sleep Duration



C130185 N75LAT N75 Latency

C117887 P100AMP P100 Amplitude

C117888 P100LAT P100 Latency

C154871 REMDUR REM Duration

C154872 REMLAT REM Latency

C154866 SKNCUDNC Skin Conductance

C154867 SOL Sleep Onset Latency

C69310 SUV Standard Uptake Value

C116141 SUVR Standard Uptake Value Ratio

C41145 THICK Thickness

C25335 VOLUME Volume

C-code

(Concept

Code)

Skin Response Test

Code

(SRTESTCD)

(codelist code =

C112024)

Skin Response Test Name

(SRTEST)


C112221 ASRINDEX Allergen Skin Response Index

C112222 ASRINT Allergen Skin Response Intensity

C122195 BLISTIND Blistering Indicator

C112283 FLARESZ Flare Size

C112281 FLRLDIAM Flare Longest Diameter

C112282 FLRMDIAM Flare Mean Diameter

C122196 IDRLDIAM Induration Longest Diameter

C41255 INTP Interpretation

C112429 WHEALSZ Wheal Size

C130186 WHLINT Wheal Diameter Interpretation

C112427 WHLLDIAM Wheal Longest Diameter

C112428 WHLMDIAM Wheal Mean Diameter

C-code

(Concept

Code)

Immunogenicity

Specimen Assessments

Test Code (ISTESTCD)

(codelist code =

C120525)

Immunogenicity Specimen Assessments

Test Name

(ISTEST)


C147272 ADA_BAB Binding Antidrug Antibody

C147273 ADA_NAB Neutralizing Binding Antidrug Antibody

C147274 ADA_NX Neutraliz Cross-React Bind Antidrug AB

C147275 ADA_X Cross-Reactive Binding Antidrug Antibody

C132360 EVIGGASC EBOV Specific IgG AB Secreting Cells

C132361 EVIGMASC EBOV Specific IgM AB Secreting Cells

C120622 H1IGGASC H1 Specific IgG Antibody Secreting Cells

C120623 H3IGGASC H3 Specific IgG Antibody Secreting Cells

C132362 IGMABSC IgM Antibody Secreting Cells

C120624 TIGGASC Total IgG Antibody Secreting Cells


• Shows the TEST and TESTCD pair on one row.

C-code

(Concept

Code)

Vital Signs Test Code

(VSTESTCD)


Vital Signs Test Name

(VSTEST)


C103346 ABSKNF Abdominal Skinfold Thickness

C16358 BMI Body Mass Index

C126083 BMR Basal Metabolic Rate

C81298 BODLNGTH Body Length

C122232 BODYFATM Body Fat Measurement

C25157 BSA Body Surface Area

C25299 DIABP Diastolic Blood Pressure

C147491 ENRGEXP Energy Expenditure

C132482 EWEIGHT Estimated Weight

C100946 FARMCIR Forearm Circumference

C49680 FRMSIZE Body Frame Size

C81255 HDCIRC Head Circumference

C25347 HEIGHT Height

C100947 HIPCIR Hip Circumference

C49677 HR Heart Rate

C117976 IDEALWT Ideal Body Weight

C84372 KNEEHEEL Knee to Heel Length

C71258 LBM Lean Body Mass

C49679 MAP Mean Arterial Pressure

C147492 MAXPREHR Maximum Predicted Heart Rate

C124475 MUARMCIR Mid-Upper Arm Circumference

C154891 NECKCIR Neck Circumference

C60832 OXYSAT Oxygen Saturation

C49676 PULSE Pulse Rate

C100945 PULSEPR Pulse Pressure

C49678 RESP Respiratory Rate

C87054 SAD Sagittal Abdominal Diameter

C98785 SSSKNF Subscapular Skinfold Thickness

C25298 SYSBP Systolic Blood Pressure

C104622 TBW Total Body Water


C98793 TRSKNF Triceps Skinfold Thickness

C17651 WAISTHIP Waist to Hip Ratio

C25208 WEIGHT Weight

C100948 WSTCIR Waist Circumference

Vital Signs Test and Test Code Pairing (a closer look)

• What should be done with FA codelists?• Broken down by therapeutic area

• What about the parent domain?

Feedback Needed:


• This would be in addition to the usual terminology files already published by NCI-EVS.

• What does the product look like?• What types of metadata do you want to see? Just the Code/Long Name/Short Name or

should we include synonyms and definitions as well?

• What file formats should we publish?

• Is this a nice-to-have or need-to-have?

Implementation Challenge #3: How do I know whether a TEST/CD or PARM/CD has controlled response values and/or associated metadata?

• A published TEST or PARM value may have response terminology:

• A single test in the EGTEST/CD codelist may have a finite set of responses located in the EGSTRESC codelist that constitutes a subset of the EGSTRESC codelist.

• In addition, a published TEST or PARM value may have associated qualifier variable terminology:

• A single test in the VSTEST/CD codelist may have a constrained set of units of measure or body positions that are valid for the numeric responses to that VSTEST/CD.

• These relationships are not readily apparent in the Controlled Terminology publication files that are produced today.


• It is inefficient to comb through 100s of rows of text within a single codelist looking for the small subset of values that are needed for a given context.

• Should CDISC define and control these subsets so that they are re-usable for everyone?


UNIT codelist =>

692 Terms!

•in•cm•m•ft

Valid Units

The Fix: Codetable Mapping Files

• To address this issue, the Controlled Terminology Teams have created Codetable Mapping Files based on published Terminology, which show relationships between terms in different Controlled Terminology codelists.

• These supplemental files provide human and machine-readable linkages between published terms across multiple codelists and may be helpful for data QA/QC, CRF building, and data mapping.

• These supplemental files are publicly reviewed, updated quarterly and are available for download on the CDISC.org controlled terminology page.

• Supporting the following domains: TU, TR, RS, CV, EG, TS, SC, VS, and DS.

• Currently in Excel format only; not programmatically generated.


Oncology Codetable Mapping Files

• Covers TU, TR, RS

• Covers RS domain for RECIST1.0, RECIST1.1, iRECIST, LUGANO

• Team working on additions: RANO (2010), and RAJKUMAR Multiple Myeloma


C-code

(Concept

Code)

Category of Oncology

Response Assessment

(ONCRSCAT)


C-code

(Concept

Code)

Oncology Response

Assessment Test Code

(ONCRTSCD)


Oncology Response

Assessment Test Name

(ONCRTS)


C-code

(Concept

Code)

Oncology Response

Assessment Result

(ONCRSR)


C124414 RECIST 1.0 C94534 TRGRESP Target Response C4870 CR

C124414 RECIST 1.0 C94534 TRGRESP Target Response C18058 PR

C124414 RECIST 1.0 C94534 TRGRESP Target Response C18213 SD

C124414 RECIST 1.0 C94534 TRGRESP Target Response C35571 PD

C124414 RECIST 1.0 C94534 TRGRESP Target Response C62222 NE

C124414 RECIST 1.0 C94535 NTRGRESP Non-target Response C4870 CR

C124414 RECIST 1.0 C94535 NTRGRESP Non-target Response C18213 SD

C124414 RECIST 1.0 C94535 NTRGRESP Non-target Response C35571 PD

C124414 RECIST 1.0 C94535 NTRGRESP Non-target Response C62222 NE

C124414 RECIST 1.0 C96613 OVRLRESP Overall Response C4870 CR

C124414 RECIST 1.0 C96613 OVRLRESP Overall Response C18058 PR

C124414 RECIST 1.0 C96613 OVRLRESP Overall Response C18213 SD

C124414 RECIST 1.0 C96613 OVRLRESP Overall Response C35571 PD

C124414 RECIST 1.0 C96613 OVRLRESP Overall Response C62222 NE

C124414 RECIST 1.0 C94536 BESTRESP Best Overall Response C4870 CR

C124414 RECIST 1.0 C94536 BESTRESP Best Overall Response C18058 PR

C124414 RECIST 1.0 C94536 BESTRESP Best Overall Response C18213 SD

C124414 RECIST 1.0 C94536 BESTRESP Best Overall Response C35571 PD

C124414 RECIST 1.0 C94536 BESTRESP Best Overall Response C62222 NE

Trial Summary Codetable Mapping File

• Represents a 1:Many relationship – 1 PARM codelist to many individual response codelists.

Subject Characteristics Codetable Mapping File

• Represents a 1:Many relationship – 1 TEST codelist to many individual response codelists.

Vital Signs Codetable Mapping Files

• There is a single vital sign test (Body Frame Size) that makes use of a response codelist (SIZE).

• The rest of the tests presume numeric responses.

• Result Units and Body Position


These files are available for download on CDISC.org:

• The Controlled Terminology teams will continue to update these files as new Terminology is published, as well as develop new domain Codetable Mapping Files.

• If you are interested in seeing specific content developed, please submit the request through the New Term Request Site.


https://ncitermform.nci.nih.gov/ncitermform/?version=cdisc

Implementation Challenge #4: How do I roll-up my collected race or ethnicity values into the FDA RACE and ETHNIC categories values?

• FDA Collection of Race and Ethnicity Data in Clinical Trials (October 26, 2016) available at http://www.fda.gov/ucm/groups/fdagov-public/@fdagov-afda-gen/documents/document/ucm126396.pdf

• CDISC is preparing a ‘white paper’ to further describe implementation considerations.

• CDASH created two new variables (CDASHIG 2.0 2017): CRACE and CETHNIC to capture collected races and ethnicities.

• Collected Races and Ethnicities may role up into categories within the RACE and ETHNIC codelists (FDA-centric).

• These relationships are not readily apparent in the Controlled Terminology publication files that are produced today.


http://www.fda.gov/ucm/groups/fdagov-public/@fdagov-afda-gen/documents/document/ucm126396.pdf

The Fix: Codetable Mapping files for Race and Ethnicity

• Contains information for how to map a collected Race or Ethnicity value to one of the FDA categories in the published RACE and ETHNIC codelists.

• Published on the CDISC website and maintained by CDISC controlled terminology team.

• Updates to mapping are publicly reviewed.


Codetables

A practical application of the model


OID Domain Variable

Variable Value Condition

Where Controlled

Terminology Applies (1)

Conditional

Value's C-

Code (1)

Conditional

Value's

Codelist C-

Code (1)

Conditional

Value's Codelist

Short Name (1)

VSTESTCD-VSSTRESU.HEIGHT.1 VS VSSTRESU VSTESTCD EQ "HEIGHT" C25347 C66741 VSTESTCD

VSTESTCD-VSSTRESU.HEIGHT.2


OID


Where Controlled


Conditional

Value's C-

Code (2)

Conditional

Value's

Codelist C-

Code (2)

Conditional

Value's Codelist

Short Name (2)

VSTESTCD-VSSTRESU.HEIGHT.1 VSTEST EQ "Height" C25347 C67153 VSTEST



OID

Variable's

Permissible

Value

Permissible

Value's C-

Code

Permissible

Value's

Codelist C-

Code

Permissible

Value's

Codelist Short

Name

VSTESTCD-VSSTRESU.HEIGHT.1 cm C49668 C66770 VSRESU

VSTESTCD-VSSTRESU.HEIGHT.2 in C48500 C66770 VSRESU

VSTESTCD-VSSTRESU.HEIGHT.3 mm C28251 C66770 VSRESU

VS Codetable – Binding Test, Test Code, and Units for Height

For Where

Use

And Where

TEST-and-

TESTCD

Binding


OID Domain Variable


Where Controlled


Conditional

Value's C-

Code (1)

Conditional

Value's

Codelist C-

Code (1)

Conditional

Value's Codelist

Short Name (1)

VSTESTCD-VSSTRESU-SYSBP-mmHg.1 VS VSSTRESU VSTESTCD EQ "SYSBP" C25298 C66741 VSTESTCD

VSTESTCD-VSSTRESU-SYSBP-mmHg.2 VS VSPOS

VSTESTCD-VSSTRESU-SYSBP-mmHg.3


OID

Variable's

Permissible

Value

Permissible

Value's C-

Code

Permissible

Value's

Codelist C-

Code

Permissible

Value's

Codelist Short

Name

VSTESTCD-VSSTRESU-SYSBP-mmHg.1 mmHg C49670 C66770 VSRESU

VSTESTCD-VSSTRESU-SYSBP-mmHg.2 DECUBITUS C77532 C71148 POSITION

VSTESTCD-VSSTRESU-SYSBP-mmHg.3 FOWLERS C62173 C71148 POSITION

VSTESTCD-VSSTRESU-SYSBP-mmHg.11 SITTING C62122 C71148 POSITION

VS Codetable – Binding Test, Test Code, Units, and Anatomic Position for Systolic Blood Pressure

OID


Where Controlled


Conditional

Value's C-

Code (2)

Conditional

Value's

Codelist C-

Code (2)

Conditional

Value's Codelist

Short Name (2)


VSTEST EQ "Systolic Blood

Pressure" C25298 C67153 VSTEST




For Where

Use

And Where

TEST-and-

TESTCD

Binding


TS Codetable – Binding Parameter, Parameter Code, Usage, and Notes for Treatment Add-On

OID


Where Controlled


Conditional

Value's C-

Code (2)

Conditional

Value's

Codelist C-

Code (2)

Conditional

Value's Codelist

Short Name (2)

Variable's

Permissible

Value

Permissible

Value's C-

Code

Permissible

Value's

Codelist C-

Code

Permissible

Value's

Codelist Short

Name

TSPARMCD-TSVAL-ADDON.1

TSPARM EQ "Added on to

Existing Treatments" C49703 C67152 TSPARM N C49487 C66742 NY

TSPARMCD-TSVAL-ADDON.2 Y C49488 C66742 NY

OID Tagged Usage Administrative Notes


FDA Desired - Clinical = "Y". Appendix B. US FDA Study Data

Technical Conformance Guide v4.2. October 2018.

Use TSVALNF for data connoting to unknown or not

applicable


For Where

UseAnd Where

PARM-and-

PARMCD

Binding

OID Domain Variable


Where Controlled


Conditional

Value's C-

Code (1)

Conditional

Value's

Codelist C-

Code (1)

Conditional

Value's Codelist

Short Name (1)


Where Controlled


TSPARMCD-TSVAL-ADDON.1 TS TSVAL TSPARMCD EQ "ADDON" C49703 C66738 TSPARMCD

TSPARM EQ "Added on to

Existing Treatments"


Description on Usage and References


TS Codetable – Binding Parameter, Parameter Code, Usage, and Notes for Current Treatment

OID Domain Variable


Where Controlled


Conditional

Value's C-

Code (1)

Conditional

Value's

Codelist C-

Code (1)

Conditional

Value's Codelist

Short Name (1)

TSPARMCD-TSVAL-CURTRT.1 TS TSVAL TSPARMCD EQ "CURTRT" C85582 C66738 TSPARMCD

OID


Where Controlled


Conditional

Value's C-

Code (2)

Conditional

Value's

Codelist C-

Code (2)

Conditional

Value's Codelist

Short Name (2)

TSPARMCD-TSVAL-CURTRT.1

TSPARM EQ "Current

Therapy or Treatment" C85582 C67152 TSPARM

OID

External

Dictionary's

Organization

External

Dictionary's

Name

External

Dictionary's

Component Tagged Usage Condition

TSPARMCD-TSVAL-CURTRT.1 US FDA

Substance

Registration

System

Unique

Ingredient

Identifier

(UNII)

FDA Desired - Clinical = "Conditional". Appendix B. US FDA

Study Data Technical Conformance Guide v4.2. October

2018.

FAQs on Electronic Study Data Submission. Table 4-6. Japan

PMDA. http://www.pmda.go.jp/english/review-

services/reviews/advanced-efforts/0007.html#Q46.

Retrieved on 2018-12-28.

US FDA: TSPARMCD =

"ADDON" AND TSVAL = "Y"

For Where

Use

And Where

PARM-and-

PARMCD

Binding

Description on Usage and References

Code Terms Mapping

How terms are mappable to a term in another codelist

Mapping of collected ethnicity (CETHNIC) to ethnicity (ETHNIC) using the same model


OID Domain Variable

Variable Value

Condition Where

Controlled

Terminology

Applies (1)

Conditional

Value's C-

Code (1)

Conditional

Value's

Codelist C-

Code (1)

Conditional

Value's Codelist

Short Name (1)

Variable's

Permissible

Value

Permissible

Value's C-

Code

Permissible

Value's

Codelist C-

Code

Permissible

Value's

Codelist Short

Name

Mapping.ETHNIC.

ETHNICC.C17459.

1 DM ETHNIC

CETHNIC EQ

"HISPANIC OR

LATINO" C17459 C128690 ETHNICC

HISPANIC OR

LATINO C17459 C66790 ETHNIC

Mapping.ETHNIC.

ETHNICC.C17459.

2 DM ETHNIC

CETHNIC EQ

"SPANISH" C67120 C128690 ETHNICC

HISPANIC OR


Mapping.ETHNIC.

ETHNICC.C17459.

3 DM ETHNIC

CETHNIC EQ

"CUBAN

AMERICAN" C67115 C128690 ETHNICC

HISPANIC OR


OID Domain Variable

Variable Value

Condition Where

Controlled

Terminology

Applies (1)

Conditional

Value's C-

Code (1)

Conditional

Value's

Codelist C-

Code (1)

Conditional

Value's Codelist

Short Name (1)

Variable's

Permissible

Value

Permissible

Value's C-

Code

Permissible

Value's

Codelist C-

Code

Permissible

Value's

Codelist Short

Name

Mapping.ETHNIC.

ETHNICC.C41222.

1 DM ETHNIC

CETHNIC EQ "NOT

HISPANIC OR

LATINO" C41222 C128690 ETHNICC

NOT

HISPANIC OR


Mapping.ETHNIC.

ETHNICC.C41222.

2 DM ETHNIC

CETHNIC EQ

"ASHKENAZI JEW" C17950 C128690 ETHNICC

NOT

HISPANIC OR


Mapping.ETHNIC.

ETHNICC.C41222.

3 DM ETHNIC

CETHNIC EQ

"SEPHARDIC JEW" C103283 C128690 ETHNICC

NOT

HISPANIC OR


For Where Maps to

For Where Maps to

Implementation Challenge #5: Can I access codelist and mapping information in QRS Supplements electronically?

• As of Q4 2018, 67% of codelists in SDTM CT package is QRS-related: 384 for Questionnaire (QS), 84 for Clinical Classification (CC), 45 for Functional Test (FT)

• QRS Supplements contain a wealth of intricate details such as codelists and terms for each measure, measure group, and measure item, as well as mapping instructions that bind terminology to SDTMIG domains and variables

• Responses are not controlled

• PDF and HTML publication formats are great for human consumption. Implementers want them to be machine-readable and accessible through SHARE for process automation


QRS

Measure Item and Response Metadata


QRS Example – Combat Exposure Scale Version 1.0 (CES01)

• Displayed is a draftannotated CRF for Combat Exposure Scale (CES01)

• CES01, a public domain measure, has 7 items

• Has 5 distinct response groups, all in Likert scale

• Items #5, 6, 7 share the same response group



• This figure shows how 1 response group metadatais shared with 3 separate items (#5, 6, 7)

• Note how each response has its metadata corresponding to SDTMIG mappings typical in QRS Supplements



• Each item will show TEST and TESTCD relationships explicitly

• So will applicable CAT, SCAT, EVALID, EVLINT

• CDISC is evaluating to also control responses for measures in public domain, i.e., assign c-codes to each response


QRS Example – Combat Exposure Scale Version 1.0 (CES01): Response Metadata

Response’s Ordinal

ORRES Value

STRESC Value

STRESN Value


QRS Example – Combat Exposure Scale Version 1.0 (CES01): Measure Item Metadata

Long Question Text

Short Question Text

TEST’s C-code

TESTCD’s C-code

Question’s Ordinal


QRS Example – Combat Exposure Scale Version 1.0 (CES01): Measure-level metadata

Measure Description

Effective Date

Publication Status (Draft)

QRS Version

QRS Long Label

QRS Short Label

QRS Type

Measure CAT’s C-code

2019 and Beyond

• Roadmap Considerations:

• Identify useful structures and formats

• Consider versioning

• Consider multiple regulators/requirements

• Consider maintenance/storage of information

• Deliverables:

• Complete all domain mappings (focus on IG3.2 and Model1.4)

• Apply content to structures and formats

• Publish!

• Continue exploring the development and production of an additional terminology product containing TEST/TESTCD and PARM/PARMCD pairings, code/decode pairings and ranking metadata.


Thanks to the teams!

• Oncology SDS Terminology Team

• General Terminology Team

• Codelist Relationships Sub-Team Active Contributors:

• Leads: Donna Sattler, Anthony Chow, Erin Muhlbradt

• Kristin Kelly – Pinnacle21

• Smitha Karra – Gilead

• Sharon Weller – Eli Lilly

• Mike Lozano – Eli Lilly

• Barbara Lentz – Bayer

• Anna Pron-Zwick – Astra Zeneca

• Judith Goud – Nurocor

• Swarupa Sudini – ICON

• Craig Zwickl – Independent

• CDISC: Diane Wold, Amy Palmer, Julie Chason


Helpful Links

• Team WIKI Site: https://wiki.cdisc.org/display/CT/CT+Relationships+Sub+Team

• Original CT Subteam Proposal: https://wiki.cdisc.org/download/attachments/52592845/ct_subteam_proposal_final_asc.pptx

• CT Relationships Kickoff Slides: https://wiki.cdisc.org/download/attachments/52592845/CT_Relationships_Subteam_kick%20off.pptx

• CDISC CT Website: https://www.cdisc.org/standards/terminology


https://wiki.cdisc.org/display/CT/CT+Relationships+Sub+Team

https://wiki.cdisc.org/download/attachments/52592845/ct_subteam_proposal_final_asc.pptx

https://wiki.cdisc.org/download/attachments/52592845/CT_Relationships_Subteam_kick off.pptx

https://www.cdisc.org/standards/terminology

Thank You!

Donna Sattler: [email protected]

Anthony Chow: [email protected]

Erin Muhlbradt: [email protected]

mailto:[email protected]



Documents

Controlled Terminology Mapping/Alignment Across Codelists Slides_1.pdf · • including domain specific variables and test level responses. •Mapping based upon SDTM 1.4, SDTMIG