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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:
32
LindaCollins:[email protected]