Dcdisc 2015-10-27 Define-XML 2 Slides

7/25/2019 Dcdisc 2015-10-27 Define-XML 2 Slides

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Define-XML 2.0.0Presented

at

DCDISC

October

27,

2015

Rockville,MD

JaneDiefenbachwithJohnBrega andLindaCollins

PharmaStatLLC


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Whatis

Define

XML,

where

did

it

come

from,

and

why

is

it

useful?

DefineXMLV1.0wasagamechanger.

DefineXMLV2.0isbetterbuthow?

Notesfrom

the

field

Whatsdifferent

ChallengesfacingDefineXMLV2.0.0producersandusers


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-

Latestversion

of

CDISC

model

to

document

databases

BasedonCDISCODMschema(xmlformat)

WorksonSDTM,SEND,ADaMandvirtuallyanyproprietarystructure

Machinereadable

and browseable with

the

right

stylesheet


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199901

General

ConsiderationsElectronic

Format.

Document ata asesusingmeta ata.Simp e spec or e ine.p .

20050205 CRTDDS/define.xmlV1.0.

ac nerea a e,muc morecomp e ean spec c an

define.pdf.Stylesheetisaproblem.

. .

metadatasoitworksbetterforADaMandsolvessomeproblemsin

SDTMdocumentation.

20130305 FinalDefineXMLV2.0, includesarobuststylesheet.Thisversionis

implementable.


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First generation, 1999e ne.p

Specification

Example


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Second generation, 2005- - -

SpecificationExample


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Third generation, 2013e ne- . . , e ne.xm

SpecificationExample


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.

Databasedocumentation

was

incomplete,

everybody

did

it

differently.

Paperandpdfdocumentation,evenonstandardizedelectronic

readthe

documentation

and

write

programs

to

execute

documented

rules.

documentation.


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with content rules, machine-readableme a a a

BecauseCDISC

authors...

Designedacommonsetofdataelementsfordatabasedocumentation(metadata)

Specifiedhowtorepresentthem

Published

the

elements

in

a

machine

readable

format Userscan...

Produce more consistent documentation for human readers

Automatedata/documentationcomparisons

Usemetadata

to

load

and

query

data

repositories


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.

Sixclasses

of

metadata:

tu yeve

Domainlevel

Variablelevel

ControlledTerminology

ComputationalMethod

Amachinereadablemodelthatcouldsu ortflat twodimensionaltablesandmultidimensionalrepresentations(linksinalldirections)

Unambiguouscontentrules(mostly)

DemoV1define.xmlanddefine.pdf,compareto1999define.pdf


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1. Thestylesheet

works!

2. Datasetscanhavecomments.Andmethods.

3. Commentscanlinkouttooneormoreexternaldocuments.

4. Value

level

metadata

can

be

more

specific

with

where

clauses.5. Codelistmetadatamodelisricher.


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Thebackbuttonisreliable

pdfoptionforprinting

DemoV1define.xmlanddefine.pdf


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Datasets can have comments. Andme o s

EXandPP,bothderiveddomains

Customdomains

Standarddomains

when

they

are

used

off

label

StudyDataReviewersGuide(SDRG)hadtomakeupforthise c ency n . . es o eep a ase me a a aw e a ase


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.

14


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15


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WindowingrulesinADRG

EXderivationfromECandDAinSDRG

Efficacydataset

construction

in

ADRG

DemoV2Commentswithexternalpage:file links


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Value-level metadata can be specific:, examp e

V1.0does

not

support

one

test

with

two

sets

of

attributes,

e.g.

SerumProteinhasacontinuousnumericresult (LBCAT=CHEMISTRY,LBSPEC=SERUM,LBSTRESC=80,LBSTRESU=mg/dL)

UrineProteinusuallyhasanordinalcharacterresult(LBCAT=URINALYSIS,LBSPEC= URINE ,LBSTRESC= +1 ,LBSTRESU=

LBTESTCD=PROTandLBTEST=Proteinforbothbuttypeisdifferentandurinalysisneedsacodelistonresultandunits

V1.0onlysupportsoneversionofvaluelevelmetadataattheTestorSuppqual level.Theresultisanonspecificmashup.


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-Example from 2.0, part 4: Same LBTESTCD different LBCAT

Variable Where Type Length/Controlled

Terms

or

Origin Derivation/Comment

Display

Format

Format

LBSTRESC LBCAT="CHEMISTRYand

LBTESTCD=BILI(Bilirubin)

Float 8 eDT

= oat e

andLBTESTCD

=

"GLUC"

(Glucose)

LBSTRESC LBCAT="URINALYSISand

LBTESTCD=BILI(Bilirubin)

text 8["1+",2+",

+3,"NEGATIVE"]

eDT

LBSTRESC LBTESTCD="GLUC"(Glucose)and

LBCAT=URINALYSIS

text 8["1+","2+","NEGATIVE",

"TRACE"]

eDT

18


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Value-level metadata can be specific:, examp e

ECGdata

can

be

continuous

or

categorical,

depending

on

the

test,

whichmightbeameasurement,afinding,oraninterpretation

V1.0onlysupportsoneversionofvaluelevelmetadatasowecould

V2.0uses

where

clauses

to

define

value

level

metadata

that

can

refer

tomanysubsetsofobservations


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-Example from 2.0, part 1: VariablelevelLinks

20


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-Example from 2.0, part 2: Value Level

21


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Value-level metadata can be specific:a

Studyendpoint

is

blood

pressure.

Various

approaches

to

imputation

producethreekindsofrecords:

Noimputation:PARAM=DIABP,DTYPE=

Lastobservationcarriedforward:PARAM=DIABP,DTYPE=LOCF

Mean

of

last

three

observations:

PARAM=DIABP,

DTYPE=MEANP3 Theserecordshavethreedifferentorigins(onetraceabletoSDTM,

. . PARAMinthevaluelevelmetadataandthethreeoriginsendup

mashed

up

in

Comments. . usesw erec auses.


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ADaM value-level metadata examplevar es y an

Display

Format

Termsor

Format

' '=

DTYPE=

''

.

AVAL PARAMCD='DIABP'and

DTYPE='LOCF'

integer 8 Derivation:VS.VSSTRESNwith

missingvaluesimputedusingthe

lastobservationcarriedforward

method.SeeADRG,page27.

AVAL PARAMCD='DIABP'and

DTYPE='MEANP3'

integer 8 Derivation:VS.VSSTRESNwith

missingvaluesimputedusingthe

meanoflastthreenonmissing

observations.SeeADRG,page28.


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ADaM value-level metadata examplevar es y an

Variable Where Type Length

Display

Format

Controlled

Termsor

Format

Source Derivation Com

ment

ADT CNSOR

=

0 date 8ISO8601da. Predecessor:

DM.DTHDTCwhere

DM.DTHFL='Y'

ADT CNSOR=1 date 8ISO8601da. Predecessor:

DM.RFPENDTCwhere

DM.DTHFL=

''


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terminology,indicatesifcodelistisextensibleornot.

DifferentiatesEnumeratedlists(Mild,Moderate,)fromo e eco e s s = , = o era e,

IdentifiescontrolledterminologybyCDISCCcode

Bettercontroloverorderingofcodelistelements.


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Example from 1.0

26


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Example from 2.0

27


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canscroungeupthemetadata.

Somethingsthatusedtobesimplebutinflexiblearenowflexibleu comp ca e .

2.0enablesmoreprecisedescriptionofyourdata,butdemandsmoredetailstoachieveit.

Thechanges

are

not

incremental

or

backwardly

compatible.

TheymakeV1Definedocumentationsystemsobsolete.


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Ori inis

different

Keyvariablesaredifferent

Newdatatypesincludingpartialandincompletedates/datetimes

MorechoicesforCommentsandMethods.Theyusedtobejusttext

strings.

Now

theyre

data

structures

that

can

also

reference

anexternaldocumentandprovidealocationreference.

Methodsneedtobenamed.Reusablerulesarebest.Methodscanhavecommentstoo.

Pagereferences

dont

need

Destinations

in

the

target

document

anymore(e.g.aCRF)


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toillustrateconcepts.Theresmuchmoregoingon.

MigratingfromDefineXMLV1.0isnotatallstraightforward.uc e ngnee e even youmapovercon en .

reviewersplease

be

patient.)

Whatvaluelevelmetadatashouldwedocument?Metadataoverlapsdata.Needsarigorousstudyofusecases.


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Neteffectisasubstantiallynewandmorecomplexxmlstructurewhichmakes1.0systemsobsolete.Wehadtoredesignoursystemop o o om.

Enhancedfunctionality

is

compelling

and

we

expect

rapid

uptake,

despitethechallengesofimplementation.


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an you

JaneDiefenbach:[email protected]

JohnBrega:

[email protected]

32

LindaCollins:[email protected]

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Dcdisc 2015-10-27 Define-XML 2 Slides