FDA (CDER) project billed as:
Make clinical observations queriable:
Metadata
Data (standards all the way down)
SELECT ?outcomeType ?dose (AVG(?endpoint-time) AS ?rate) WHERE { # drug of interest ?adminDrug dt:CD.displayName "Upsidasium" ; … codingSystem … . # subjects in studies about drug ?arm :studySubject ?adminDrug ; :studyParticipation ?subject . # demographic selection ?subject :taxon ncbitax:9606 . # outcomes assessing prescription performance ?outcome :intervention ?p ; :value [ a ?outcomeType ] . # ... of that drug on that subject (participation) ?p a :Prescription ; :involvedSubject ?subject ; :medication ?adminDrug . } ORDER BY ?dose
Establish common study data standards:
Success Criteria at end of the 5-year PDUFA V period:
code everything
minimize:
cope gracefully with:
interoperate with EHRS:
Existing Models/Standards
Controlled Terminologies:
Therapeutic Efficacy is comprised of:
How is clinical data submitted today?
All lean on lists of study/domain-specific terms.
Issues:
bridg:PerformedObservation
Portable BRIDG Representation
:SerumCreatinineLevel a owl:Class ; rdfs:subClassOf [ owl:onProperty bridg:resultIn ; owl:allValuesFrom bridg:PerformedClinicalResult ], [ owl:onProperty bridg:resultIn ; owl:cardinality 1 ] .
:GraftBPARAssessment a owl:Class ; rdfs:subClassOf core:NegativeOutcome ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:onProperty core:afterIntervention ; owl:someValuesFrom [ a owl:Restriction ; owl:onProperty core:hasPathologyFinding ; owl:hasValue :BanffIII ] ] [ a owl:Restriction ; owl:onProperty core:hasResultValue ; owl:hasValue :NonFunctioningGraft ] ) ] .
<http://www.w3.org/2013/12/FDA-TA/RenalTransplantation> a owl:Ontology ; owl:imports <http://www.w3.org/2013/12/FDA-TA/core> , <http://www.w3.org/2013/12/FDA-TA/renal> , <http://www.w3.org/2013/12/FDA-TA/transplant> .
Make clinical observations queriable:
?arm :studySubject ?adminDrug
SELECT ?outcomeType ?dose (AVG(?endpoint-time) AS ?rate) WHERE { # drug of interest ?adminDrug dt:CD.displayName "Upsidasium" ; … codingSystem … . # subjects in studies about drug ?arm :studySubject ?adminDrug ; :studyParticipation ?subject . # demographic selection ?subject :taxon ncbitax:7609 . # outcomes assessing prescription performance ?outcome :intervention ?p ; :value [ a ?outcomeType ] . # ... of that drug on that subject (participation) ?p a :Prescription ; :involvedSubject ?subject ; :medication ?adminDrug . } ORDER BY ?dose
:subjectspostOpDay3GFR a rrej:RenalFunctionObservation ;
mm:observationTime "2013-07-08T14:50:00"^^xsd:dateTime ;
rrej:gfrFlowRate [ data:value 12.0 ; data:units ucum:mL-per-minute ].
:subjectsCSAR1 a rrej:RenalFunctionDiagnosis ; mm:observationTime "2013-07-08T14:52:00Z"^^xsd:dateTime ;
mm:isSupportedBy :subjectspostOpHour36GFR , :subjectsPostOpDay3UrineOutput , :subjectsPostOpDay3Temperature ,
:subjectsPostOpDay3SiteTenderness , :subjectsPostOpDay3SCr , :subjectspostOpDay3GFR .
:subjectsRenalBiopsy1 a rrej:RenalBiopsy ; mm:observationTime "2013-07-08T15:35:00Z"^^xsd:dateTime ;
mm:isJustifiedBy :subjectsCSAR1 ;
mm:labReport :subjectsRenalBiopsy1report .
:subjectsRenalBiopsy1report a rrej:RenalBiopsyReport ; mm:observationTime "2013-07-08T16:10:00Z"^^xsd:dateTime ;
mm:pathologyFinding rrej:BanffIII .
Would be in a table with codes in an EMR:
obs id | when | coding system | ObsCode | value | units | addressing…performer… |
---|---|---|---|---|---|---|
1234 | 2013-07-08T14:50:00 | CPT | 82565 | 12 | mL-per-minute | |
5678 | 2013-07-08T14:50:00 | SNOMED 2014-01-01 | 241374009 | 12 | mL-per-minute | |
4321 | 2013-07-08T14:50:00 | LOINC | 48643-1 | 12 | mL-per-minute |
or C-CDA:
<observation classCode="OBS" moodCode="EVN"> <code code="48643-1" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Glomerular filtration rate/1.73 sq M.predicted.black" /> <effectiveTime value="201307081450"/> <value type="PQ" value="12.0" unit="mL/min"/> <interpretationCode/> <referenceRange /> </observation>
_:obsX bridg:PerformedObservationCode [ hl7:coding [ dt:CDCoding.code "48643-1" ; dt:CDCoding.codeSystem "2.16.840.1.113883.6.1" ; dt:CDCoding.codeSystemName "LOINC" ; dt:CDCoding.displayName "Glomerular filtration rate/1.73 sq M.predicted.black" ] ].vs.
_:obsX bridg:PerformedObservationCode loinc:48643-1 .
A "subject" is a subject participation.
Activities come in four flavors e.g.
How do I link a bridg:Drug
to an bridg:PerformedSubstanceAdministration
?
:RenalFunctionObservation rdfs:subClassOf mm:QuantitativeMeasurement . :RenalBiopsy rdfs:subClassOf mm:DiagnosticProcedure , [ owl:onProperty mm:isJustifiedBy ; owl:minCardinality 1 ] , [ owl:onProperty mm:labReport ; owl:cardinality 1 ] . :RenalBiopsyReport rdfs:subClassOf mm:PathologyReport , [ a owl:Restriction ; owl:onProperty :pathologyFinding ; owl:someValuesFrom [ owl:oneOf ( :banfI :banfII :banfIII ) ] ] .
These don't capture: