FDA-TA Acceptance Criteria

7 Jan, 2014

Schemas so far...

: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 ) ] ] .

Clinical Schemas

O-RIM - HL7 Reference Information Model + Datatypes, etc
Computer-Based Patient Record -
latent ontology implied by FHIR-RDF

These don't capture:

outcomes (discriminated from Observations)
1st class predicates (gfrFlowRate, serumCreatinine)
... specializations in general

Specializations

: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
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

Precedents in LifeSci

UNIPROT - used like SQL Schema
EBI interfaces
Gene Ontology Annotations - data itself in the ontology language
OpenPhacts - schema over wide domain
... 10s or little schemas like MIAME

wants:

metadata

propagate structure from SMEs to CROs/submitters
eliminate ambiguities and synonyms
enables search across studies

data

define model AND FORMAT
normalize terminology
data unification/integration

Latter, maybe both, need to include protocols in sufficient detail that the intersection can be computed and queried.