Eric Prud'hommeaux, <W3C/MIT>
With material from:
Health Care & Life Sciences IG, <public-semweb-lifesci@w3.org>
Outsource risk to startups
VCs make the early go/no-go decisions.
Pharmas left with manufacturing development and distribution.
Practically, we want information available to
improve clinical research and clinical care.
The hard job is communicating context.
Everyone thinks their model should be the over-arching model
(or they go work on another one).
What are the characteristic of a model?
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
ID: 23453 name: George Andrew Tour demographics DOB: 1934-05-15 gender: Male presriptions 1 no earlier than: 2009-05-15 ndc: 00007414020 generic name: COREG TABLETS … conditions 1 no later than: 2009-05-15T12:00:00 ICD9: 410 common name: hypertension … encounters 1 date: 2009-05-15 reported symptoms: none working diagnosis: none tests 1 no earlier than: 2009-05-15T12:00:00 CPT: 85025 common name: Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count 1 CPT: 85014 LOINC: 41654-5 common name: Hematocrit value: 38.0 units: percent 2 CPT: 78720 LOINC: 30428-7 common name: Mean Corpuscular Volume value: 97.4 units: fl …
wing it- make up new names as they're needed.
not distributable.
HL7 approach: Reference Information Model (RIM) @@image allowed?
constrained by Refined Message Information Models (R-MIMs).
Implementable Technology Specifications (ITS) is syntactic restrictions (schema) while R-MIM is a model restriction?
Some desirable features:
EMR uptake low and fragmented.
Can EHRs be as practical as Quicken?
Very low, have to focus on success stories.
Brute force -- acquire data and read lots of documentation.
Force into common framework
(either the publisher/custodian or the user may get stuck with this job).
Mimic DB, Machine-learning, @@Peter
Moving data between Clinical Data Repositories (CDRs):
@@example of Hematocrit and Mean Corpuscular Volume with random Z-segment extensions - Lloyd? Charlie?@@
@@pack some HTML and coded data in here@@
The "always-human-readable" aspect is key to success.
@@p...@@
observation_fact
observation_fact
concept | name_char | valtype_cd | nval_num | units_cd |
---|---|---|---|---|
4544-3 | Haematocrit | N | 0.55 | N/A |
787-2 | Mean Cell Volume | N | 99 | fL |
The value of the latent interoperability of data depends on the quality of the data.
<obs9> sp:labName [ a sp:CodedValue ; sp:code <http://purl.bioontology.org/ontology/LNC/787-2> ; dcterms:title "Serum sodium" ; sp:codeProvenance [ a sp:CodeProvenance ; sp:sourceCode <codes#_02341> ; dcterms:title "Mean Corpuscular Volume" ; sp:translationFidelity <http://smartplatforms.org/terms/code/fidelity#automated>l . ] ] .
[ trans:testCode [ trans:x_3 "MCV" ; trans:LOINC "787-2" ; trans:description "Mean Cell Volume" ; trans:value 97.4 ; trans:units "fl" ] ] .
[ a :Result ; :name [ a :Coding ; :code "787-2" ; :system <urn:hl7-org:sid/loinc> ; :display "Mean Cell Volume" ] ; :valueQuantity [ :value 99 ; :units "fL" ; :code "fL" ; # @@ same as units? :system <urn:hl7-org:sid/ucum> ] ; :flag "+" ; :status "final" ; :referenceRanges [ a :ReferenceRange ; :rangeInterval [ :low [ :value 80 ; :units "fL" ; :code "fL" ; :system <urn:hl7-org:sid/ucum> ] ; :high [ :value 98 ; :units "fL" ; :code "fL" ; :system <urn:hl7-org:sid/ucum> ] ] ] ]
# _:mcvComp a M0:Component2 ; M0:Component2.typeCode "COMP" ; M0:Component2.contextControlCode "AP" ; M0:Component2.observationEvent _:mcvObsEvt . _:mcvObsEvt a M0:ObservationEvent ; M0:ObservationEvent.classCode "OBS" ; M0:ObservationEvent.moodCode "EVN" ; M0:ObservationEvent.code _:mcvObsEvt_CD . _:mcvObsEvt_CD a DT:CD ; DT:CD.code "787-2" ; DT:CD.codeSystem "urn:hl7-org:sid/loinc" ; DT:CD.displayName _:mcvDispName . _:mcvDispName a DT:ST ; DT:ED.value "Mean Cell Volume" . _:mcvObsEvt M0:ObservationEvent.statusCode [ a DT:CD ; DT:CD.code "completed" ] . _:mcvObsEvt M0:ObservationEvent.value [ a DT:PQ ; DT:QTY.originalText [ a DT:ED ; DT:ED.value "99 fL" ] ; DT:PQ.unit [ a DT:CD ; DT:CD.code "fL" ] ; DT:PQ.value "99" ] . _:mcvObsEvt M0:ObservationEvent.interpretationCode [ a DT:DSET ; DT:COLL.items _:b0x1184590 ] . _:b0x1184590 a rdf:Bag ; rdf:li [ a DT:CD ; DT:ANY.nullFlavor [ a DT:CD ; DT:CD.code "UNC" ] ; DT:CD.code "+" ] . _:mcvObsEvt M0:ObservationEvent.referenceRange [ a rdf:Bag ; rdf:li [ a M0:ReferenceRange ; M0:ReferenceRange.typeCode "REFV" ; M0:ReferenceRange.interpretationRange _:mcvRefIntrpLow ] ; rdf:li [ a M0:ReferenceRange ; M0:ReferenceRange.typeCode "REFV" ; M0:ReferenceRange.interpretationRange _:mcvRefIntrpHigh ] ]. _:mcvRefIntrpLow a M0:InterpretationRange ; M0:InterpretationRange.classCode "OBS" ; M0:InterpretationRange.moodCode "EVN.CRT" ; M0:InterpretationRange.value [ a DT:PQ ; DT:PQ.value "80" ; DT:QTY.originalText [ a DT:ED ; DT:ED.value "80 fL" ] ; DT:PQ.unit [ a DT:CD ; DT:CD.code "fL" ] ] ; M0:InterpretationRange.interpretationCode [ a DT:CD ; DT:CD.code "L" ; DT:CD.codeSystem "2.16.840.1.113883.5.83" ] . _:mcvRefIntrpHigh a M0:InterpretationRange ; M0:InterpretationRange.classCode "OBS" ; M0:InterpretationRange.moodCode "EVN.CRT" ; M0:InterpretationRange.value [ a DT:PQ ; DT:PQ.value "98"; DT:QTY.originalText [ a DT:ED ; DT:ED.value "98 fL" ] ; DT:PQ.unit [ a DT:CD ; DT:CD.code "fL" ] ] . _:mcvRefIntrpHigh M0:InterpretationRange.interpretationCode [ a DT:CD ; DT:CD.code "H" ; DT:CD.codeSystem "2.16.840.1.113883.5.83" ] .
How can we take advantage of "semantic" representations?