lab data modeling options lab loinc meeting june, 2015 indianapolis, indiana
TRANSCRIPT
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Lab Data Modeling Options
Lab LOINC MeetingJune , 2015
Indianapolis, Indiana
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CIMI and HSPC
• Clinical Information Modeling Initiative (CIMI)– International organization for making “logical”
models for interoperability• Healthcare Services Platform Consortium (HSPC)– Defining service APIs to support truly interoperable
software
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IsoSemantic Models – Example of Problem
e.g. “Suspected Lung Cancer”
(from Dr. Linda Bird)
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Data Comes in Different Shapes and Colors
Finding – Suspected Lung Cancer
Finding – Suspected CancerLocation – Lung
Finding – CancerLocation – LungCertainty – Suspected(Let’s say this is the preferred shape)
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Data Standardized in the Service
Shape and color of data in the local database
Shape and color translation
Application
Data in preferred shape and color
Application and User
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Partial Interoperability
TermTranslators
Standard Terms(Non-standard Structure)
Application and User
Application
Local databases,CDA, HL7 V.2, etc.
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Preferred Strategy – Full Interoperability
Local databases,CDA, HL7 V.2, etc.
Term andStructureTranslators
Application
Standard StructureAND Standard Terms
(As defined by CIMI Models)
Application and User
Requ
irem
ents
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Reasons to do it on the server side
• Person writing the translation is most likely to understand the meaning of the data in their own database.
• The person writing the translation only has to understand their own data and the preferred model.– They can optimize query execution for their own system
• The query for the data is simpler. If the application has to write a query that will work for all shapes, the query will be inefficient to process by every system.
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Reason for Modeling
• Models are defined so that when a program needs to access patient data it knows the precise logical structure of the data, and the exact codes that are allowed.
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Request from CIMI to LOINC
• Create “methodless” LOINC codes where they don’t exist for the top 2000 lab LOINC codes
• This would be about 500 new LOINC codes
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Options for Data Representation(Glucose in blood by manual test strip)
Option 1PreCoordinatedGlucoseModel name (focus): 2341-6 (Glucose [Mass/volume] in Blood by Test strip manual) data.value: 120 mg/dL
Option 2PostCoordinatedGlucoseModel 1 name (focus): 2341-6 (Glucose [Mass/volume] in Blood by Test strip manual) method (qual): 1234 Test strip manual data.value: 120 mg/dL
Option 3PostCoordinatedGlucoseModel 2 name (focus): 2339-0 (Glucose [Mass/volume] in Blood) method (qual): 1234 Test strip manual data.value: 120 mg/dL
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Options
Option 4PostCoordinatedGlucoseModel 3 name (focus): (2341-6 OR 2339-0) --- Either a pre or a post coordinated code is allowed method (qual): 1234 Test strip manual data.value: 120 mg/dL
Option 5PostCoordinatedGlucoseModel 4 name (focus): (2341-6 OR 2339-0) --- Either a pre or a post coordinated code is allowed method (qual): 1234 Test strip manual component: Glucose specimen: BLD property: MCNC scale: QN data.value: 120 mg/dL
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Raw LOINC CodesCode Component Prop System Scale Method 2339-0 Glucose MCnc Pt Bld Qn mg/dL Glucose
[Mass/volume] in Blood
2341-6 Glucose MCnc Pt Bld Qn Test strip manual
mg/dL Glucose [Mass/volume] in Blood by Test strip manual
2340-8 Glucose MCnc Pt Bld Qn Test strip automated
mg/dL Glucose [Mass/volume] in Blood by Automated test strip
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QN Lab “Universal” - 1Example 1 – Quantitative lab tests with method and challengeAbstract Model
PostCoordinatedQuantLabUnivModel name (focus): [value set of QN Lab LOINC items where method and challenge is not specified] method (qual): [value set of all valid quantitative lab methods] challenge (mod): [value set of all valid challenge concepts] data.value.units: [value set of all quantitative lab units of measure]
Item to be represented: Glucose [Mass/volume] in Blood
Leaf level post coordinated QN lab model (no method) – CIMI preferred modelPostCoordinatedGlucoseModel name (focus): LN 2339-0 (Glucose [Mass/volume] in Blood) data.value.units: SCT 258797006 (mg/dL)
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QN Lab “Universal” - 2Example 1 – Quantitative lab tests with methodAbstract Model
PostCoordinatedQuantLabUnivModel name (focus): [value set of QN Lab LOINC items where method and challenge is not specified] method (qual): [value set of all valid quantitative lab methods] challenge (mod): [value set of all valid challenge concepts] data.value.units: [value set of all quantitative lab units of measure]
Item to be represented: Glucose [Mass/volume] in Blood by Test strip manual
Leaf level post coordinated QN lab model and method – CIMI preferred modelPostCoordinatedGlucoseModel – (model meaning binding, id code at the model level, should be the same for both the pre and post coordinated models) name (focus): LN 2339-0 (Glucose [Mass/volume] in Blood) method (qual): CIMISCT 1111 Test strip manual (117021008 Test strip method) data.value.units: SCT 258797006 (mg/dL)
Leaf level pre coordinated QN lab model and method – CIMI iso-semantic modelPreCoordinatedGlucoseModel name (focus): LN 2341-6 (Glucose [Mass/volume] in Blood by Test strip manual) data.value.units: SCT 258797006 (mg/dL)
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QN Lab “Universal” - 3Example 1 – Quantitative lab tests with challengeAbstract Model
PostCoordinatedQuantLabUnivModel name (focus): [value set of QN Lab LOINC items where method and challenge is not specified] method (qual): [value set of all valid quantitative lab methods] challenge (qual): [value set of all valid challenge concepts] data.value.units: [value set of all quantitative lab units of measure]
Item to be stored: Glucose [Mass/volume] in Serum or Plasma --1.5 hours post 0.5 g/kg glucose IV
Leaf level post coordinated QN lab model and challenge – CIMI preferred modelPostCoordinatedGlucoseChallengeModel name (focus): LN 2339-0 (Glucose [Mass/volume] in Blood) challenge (qual): CIMISCT 2222 (1.5H post 0.5 g/kg glucose IV) data.value.units: SCT 258797006 (mg/dL)
Lead level pre coordinated QN lab model and challenge – CIMI iso-semantic modelPreCoordinatedGlucoseChallengeModel name (focus): LN 1492-8 (Glucose [Mass/volume] in Serum or Plasma --1.5 hours post 0.5 g/kg glucose IV) data.value.units: SCT 258797006 (mg/dL)
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QN Lab “Universal” - 4Example 1 – Quantitative lab tests with mehtod and challengeAbstract Model
PostCoordinatedQuantLabUnivModel name (focus): [value set of QN Lab LOINC items where method and challenge is not specified] method (qual): [value set of all valid quantitative lab methods] challenge (qual): [value set of all valid challenge concepts] data.value.units: [value set of all quantitative lab units of measure]
Item to be stored: Glucose [Presence] in Urine by Test strip --1.5 hours post 75 g glucose PO
Leaf level post coordinated QN lab model method and challenge – CIMI preferred modelPostCoordinatedGlucoseChallengeAndMethodModel name (focus): LN 2349-9 (Glucose [Presence] in Urine) method (qual): CIMISCT 1111 Test strip manual (117021008 Test strip method) challenge (qual): CIMISCT 3333 (1.5H post 75 g glucose PO) data.value.code: [value set binding for Present/Absent]
Lead level pre coordinated QN lab model method and challenge – CIMI iso-semantic modelPreCoordinatedGlucoseChallengeAndMethodModel name (focus): LN 6763-7 (Glucose [Presence] in Urine by Test strip --1.5 hours post 75 g glucose PO by Test Strip) data.value.code: [value set binding for Present/Absent]
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Rationale for Request
• To support the CIMI preferred way of representing data we need “methodless” LOINC codes
• These codes would sometimes be useful for ordering
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Post Coordinated Specimen Lab “Universal” - 1
Common situations where specimen type is XXX: microscopic exams, antigens, antibodies, DNA, RNA, cultures (need to verify that there is an automated method for determining these classes of items)
Example 1 – Lab test with post coordinated specimen and methodAbstract Model
PostCoordinatedSpecimenLabUnivModel name (focus): [value set of labs where test is one of the types listed above] specimen (qual): [value set of all valid specimen types] method (qual): [value set of all valid lab methods] data.value.code: [value set binding]
Item to be stored: Arthropod identified in Unspecified specimenLeaf level post coordinated lab model specimen and method – CIMI preferred model
PostCoordinatedArthropodIdentifiedModel name (focus): 10644-3 (Arthropod identified ) data.value.code: [value set binding for Arthropod Answers]
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Post Coordinated Specimen Lab “Universal” - 2Example 1 – Lab test with post coordinated specimen and methodAbstract Model
PostCoordinatedSpecimenLabUnivModel name (focus): [value set of labs where test is one of the types listed above] specimen (qual): [value set of all valid specimen types] method (qual): [value set of all valid lab methods]
Item to be stored: Arthropod identified in Unspecified specimen by Permanent mount
Leaf level post coordinated lab model specimen and method – CIMI preferred modelPostCoordinatedArthropodIdentifiedModel name (focus): 10644-3 (Arthropod identified) method (qual): CIMISCT 3333 (Permanent mount) data.value.code: [value set binding for Arthropod Answers]
Leaf level precoordinated lab model specimen and method – CIMI isosemantic modelPreCoordinatedArthropodIdentifiedPermMountModel name (focus): 14787-6 (Arthropod identified in Unspecified specimen by Permanent mount)
data.value.code: [value set binding for Arthropod Answers]
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Post Coordinated Specimen Lab “Universal” - 3Example 1 – Lab test with post coordinated specimen and methodAbstract Model
PostCoordinatedSpecimenLabUnivModel name (focus): [value set of labs where test is one of the types listed above] specimen (qual): [value set of all valid specimen types] method (qual): [value set of all valid lab methods]
Item to be stored: Chlamydia trachomatis DNA [Presence] in Cervix by Probe and target amplification method
Leaf level post coordinated lab model specimen and method – CIMI preferred modelPostCoordinatedCTrachomatisDNACervixProbe name (focus): CIMISCT 1234 (Chlamydia trachomatis DNA [Presence]) specimen (qual): SCT 110949001 (Cervix cytology material) method (qual): CIMISCT 5555 (Probe and target amplification) data.value.code: [value set binding for Present/Absent]
Leaf level precoordinated lab model specimen and method – CIMI isosemantic modelPreCoordinatedCTrachomatisDNACervixProbe name (focus): 21190-4 (Chlamydia trachomatis DNA [Presence] in Cervix by Probe and target amplification method)
data.value.code: [value set binding for Present/Absent]