Modelling Taskforce Report

Modelling Taskforce Report

Dr Linda Bird19th January 2013

Agenda

• Background• Overview of modelling approach• Laboratory Results Report

• Submitted models• Comparative analysis• Modelling patterns• Clinical Models

• Terminology binding• Demographics Model• Future work and discussion

Background

Core Members:• Linda Bird (chair)• Tom Beale• Dave Carlson• Stephen Chu• Stan Huff• Mike Lincoln• Rahil Qamar Siddiqui• Gerard Freriks• Josh Mandel• Mark Shafarman• Michael van der Zel

Secretary:• Eithne Keelaghan

Taskforce MembersTechnical Resources:• Peter Hendler• Galen Mulrooney• Daniel Karlsson• Cecil Lynch• Joey Coyle• Grahame Grieve• Dipak Kalra• David MonerClinical Modelling Resource:• William Goossen• Jay Lyle• Ian McNicoll• Anneke Goossen• Heather Leslie• Sarah Ryan• Harold Solbrig• Marcelo Rodrigues dos Santos

To develop a CIMI modelling methodology, style guide and a set of models, which

together demonstrate and test the approach to CIMI clinical modelling.

Mission

This taskforce has been established to:• Further develop CIMI's modelling methodology;• Create an initial set of CIMI clinical models;• Further test and develop CIMI technical models,

including:– CIMI reference model– Archetype Object Model 1.5, and – CIMI terminology.

Terms of Reference

May 10 - 12 Meeting in Pleasanton Modelling Taskforce was established

May to Sep Taskforce infrastructure and planning; Modelling methodology; Observation modelling pattern; Heart rate model

Sept 14 - 16 Meeting in Rockville Modelling priorities: Lab Results Report(followed by Immunizations and Body

Temperature)

Oct to Dec Replanning and review of submitted Lab Result models Design Lab Results model structure and modelling patternsLab Results - Comparative analysis spreadsheetCIMI Terminology subgroup established October 2012

• Terminology binding use cases, requirements, options, proposal• Lab Results terminology semantic bindings• Lab Results terminology reference sets started• Terminology server requirements

Review of CIMI Demographics Reference Model & model analysis

Dec 2 – 4 Taskforce meeting in Groningen Lab Results comparative analysis, mindmaps, implementation, terminology binding, reference model, instances and planning

Modelling Taskforce History (2012)

Overview of CIMI Modelling Approach

CIMI Architectural Overview

CIMI Reference Model - Core

class CIMI Core Reference Model (logical)

COMPOSITION

+ category :CODED_TEXT+ language :CODED_TEXT+ territory :CODED_TEXT

CONTENT_ITEM

ENTRY

+ language :CODED_TEXT

SECTION

ARCHETYPED

+ archetype_id :ARCHETYPE_ID+ template_id :TEMPLATE_ID [0..1]+ rm_version :String = 1.0.8 {readOnly}

LOCATABLE

+ archetype_node_id :String+ name :TEXT+ uid :UID_BASED_ID [0..1]

LINK

+ meaning :TEXT+ target :EHR_URI+ type :TEXT

ITEM

ELEMENT

+ null_flavor :CODED_TEXT [0..1]+ value :DATA_VALUE [0..1]

CLUSTER

+ structure_type :CODED_TEXT [0..1]

PARTICIPATION

+ function :CODED_TEXT+ time :INTERVAL_VALUE<DATE_TIME> [0..1]+ mode :CODED_TEXT+ details :ITEM [0..*]

PARTY_PROXY

+participation

0..*

+item0..*

+content

0..*

+data1..*

+item1..*

+party1..1

+archetype_details

0..1

+link

0..*

CIMI Reference Model – Data Values class CIMI Data Value Types (logical)

YESNO

+ value :Boolean

DATA_VALUE

IDENTIFIER

+ id :String+ type :CODED_TEXT+ issuer :String

ENCAPSULATED

MULTIMEDIA

+ alternate_text :String [0..1]+ data :Byte [0..*] (Array)+ integrity_check :Byte [0..*] (Array)+ media_type :CODED_TEXT+ uri :URI [0..1]

PARSABLE

+ formalism :CODED_TEXT+ value :String

COUNT

+ value :Integer

QUANTITY

+ value :Double+ units :CODED_TEXT+ precision :Integer [0..1]

PROPORTION

+ numerator :Real+ denominator :Real+ precision :Integer [0..1]+ type :CODED_TEXT

ORDINAL

+ symbol :CODED_TEXT+ value :Integer

ORDERED_VALUE

QUANTIFIED

+ value_status :String [0..1]

AMOUNT

+ accuracy :Real [0..1]+ accuracy_is_percent :Boolean [0..1]

DATE

+ value :String

TIME

+ value :String

DATE_TIME

+ value :StringDURATION

+ duration_text :String [0..1]

TEMPORAL

TEXT

+ value :String+ language :CODED_TEXT [0..1]

URI

+ value :String

CODED_TEXT

+ code :String+ terminology_id :TERMINOLOGY_ID+ terminology_version :String [0..1]+ term :String [0..1]+ term_id :String [0..1]

EHR_URI

T : ORDERED

INTERVAL_VALUE

+ upper_unbounded :Boolean+ lower_unbounded :Boolean+ upper_included :Boolean+ lower_included :Boolean

TERM_MAPPING

+ match :Character+ purpose :CODED_TEXT [0..1]

PLAIN_TEXT

MatchRefSet

> = < ?

QuantifiedValueStatusRefSet

= < > <= >= ~

{units constrained to units of time}

+lower<T>

0..1

+mapping

0..*

+upper<T>0..1

+target 1..1

CIMI Reference Model – Demographics class CIMI Demographics Model (logical)

«archetype_parent»LOCATABLE


PARTY_RELATIONSHIP

+ source :PARTY_REF+ target :PARTY_REF+ time_validity :INTERVAL_VALUE<DATE> [0..1]+ details :ITEM [0..*]

PARTY

+ uid :HIER_OBJECT_ID+ reverse_relationship :LOCATABLE_REF [0..*]+ details :ITEM [0..*]

ROLE

+ time_validity :INTERVAL_VALUE<DATE> [0..1]+ role_type :CODED_TEXT

ACTOR

+ actor_type :CODED_TEXT+role

+relationship

0..*

Archetype Object Model (AOM)

CIMI Modelling Layers

Reference Model

PatternsMaterial Entity,

Observable, Action,Schedule, Address,

Observation,Action Clinical List Clinical Report,

Event Summary

Clinical Models Medication Item Blood Pressure Medication List Laboratory Results Report

Specialty Context Paediatric Medication Item

Neonatal Blood Pressure

Cardiology Medication List

Biochemistry Laboratory Results

Report

CLUSTER ENTRY SECTION COMPOSITION

Care Setting Context

G.P. Dispensed Medication Item

Home Blood Pressure

Outpatient Clinic Current Medication

List

Inpatient Discharge Summary

Implementation Purpose Context

Dispensed Medications GUI

Neonatal Blood Pressure in EHR

Current Medication List in EHR

Laboratory Report Message

Use Case Context Dispensed Medication Item

Standing Blood Pressure

Current Medication List

Full Blood Count Results Report

• Modular for reusability• Composable for meeting use-cases• Pattern-based for consistency• Maximal for completeness• Logical for implementation in multiple formats• Constraint-based to allow specialisation• Extensible for local requirements• Bound to terminology for isosemanticity &

interoperability

CIMI’s Modeling Approach

• Foundations1. CIMI Reference Model2. Archetype Object Model3. CIMI Modelling Patterns4. CIMI Style Guide

• Modelling Approach1. Analyse clinical models submitted (with value sets)2. Identify maximal set of data elements3. Remove ‘out of scope’ data elements (Style Guide)4. Select appropriate CIMI Modelling Patterns(Style Guide)5. Define CIMI model (Mindmap, ADL, UML)6. Add Terminology bindings

o Meaning (nodes, node relationships)o Value sets (maximal set from submitted models)

7. Add Example Model Data Instances8. Technical Validation

o ADL, UML

9. Clinical Validation / Review10. Confirm mappings from submitted models

Modelling Methodology

Laboratory Results Report

• FHIR Lab Report resource

• Intermountain Standard Lab Obs• NEHTA Pathology

Test Result• MOHH Investigation

Composition• HL7 Clinical Care

Document• Netherlands (NFU) Lab Results• EN13606 Association Lab Test• Canada InfoWay HL7 v3

POLB_MT004000UV

Submitted Models

FHIR – Lab Report resource

Intermountain – Standard Lab Obs

NEHTA – Pathology Test Result

MOHH – Investigation Composition

HL7 Clinical Care Document - Results

NFU – Lab Results

EN13606 Association – Lab Test

Canada InfoWay – HL7 v3 POLB_MT004000UV

CIMI Laboratory Results Report Design

Lab Results Report (Composition)

Test Result Group/Item (Cluster)

Lab Report Header (Entry)

Patient Encounter Summary (Entry)

Lab Test Request Summary (Entry)

Lab Test Result (Entry)

Reference Range (Cluster)

0..*

0..*

0..*

0..*

1

0..1

Specimen (Cluster)

0..*

Specimen (Cluster)

0..*

Identify maximal set of data elements

Data Element Data Type / Class Cardinality Description

Laboratory report header ENTRY 1 Information pertaining to the whole

lab report

Patient encounter summary ENTRY 0..1

Information about the patient encounter to which this report is

related.

Laboratory test request summary ENTRY 0..* The set of lab orders associated with

the lab results in this report.

Laboratory test result ENTRY 1..* Results grouped by specimen/kind/category

• Comparative analysis of submitted models is used to identify the maximal set of relevant data elements for each model (see spreadsheet)

Archetype Map forLaboratory Results Report


Composition:

Entry:

Laboratory Report Header

Patient Encounter Summary

Laboratory Test Request Summary

Laboratory Test Observation



Composition:

Entry:

Cluster:





Action

Laboratory Test Request

Laboratory Test Observable

Laboratory Test Result Group


Action

Action

Reference Range

Specimen

Action

COMPOSITION modelling patterns


Clinical Report

COMPOSITION

constrains

constrains

CIMI-COMPOSITION.laboratory_results_report

class CIMI Core Reference Model

COMPOSITION

+ category :CODED_TEXT+ language :CODED_TEXT+ territory :CODED_TEXT

CONTENT_ITEM

ARCHETYPED


LOCATABLE


LINK


PARTICIPATION

+ function :CODED_TEXT+ time :INTERVAL_VALUE<DATE_TIME> [0..1]+ mode :CODED_TEXT

PARTY_PROXY

+participation

0..*

+content 0..*

+links

0..*

+party

1..1

+archetype_details

0..1

constrains

constrains

ENTRY modelling patterns

Clinical Report Header





Clinical Entry

Observation Request

Request

Clinical Activity Observation

ENTRY

constrains

constrainsconstrains

constrains

constrains constrains constrains

constrains

constrains

constrains

CIMI-ENTRY.clinical_entry class CIMI Core Reference Model

CONTENT_ITEM

ENTRY

+ language :CODED_TEXT

ARCHETYPED


LOCATABLE


LINK


ITEM

PARTICIPATION


PARTY_PROXY

+participation

0..*

+data

1..*

+links

0..*

+party

1..1

+archetype_details

0..1

CIMI-ENTRY.laboratory_report_header

Clinical Entry

ENTRY

CIMI-ENTRY.patient_encounter_summary

Clinical Entry

ENTRY

CIMI-ENTRY.laboratory_test_request_summary

Clinical Entry

ENTRY

CIMI-ENTRY.laboratory_test_observation

Clinical Entry

ENTRY



Composition:

Entry:

Cluster:





Action





Action

Action

Reference Range

Specimen

Action

CLUSTER modelling patterns

Finding

Observable Material Entity

Action

CLUSTER

constrains

constrainsconstrains




Reference Range

Specimen

constrains

constrains constrains

constrains

Specimen Collection Site

CIMI-CLUSTER.laboratory_test_observable class CIMI Core Reference Model

CONTENT_ITEM

ARCHETYPED


LOCATABLE


LINK


ITEM

CLUSTER

+ structure_type :CODED_TEXT [0..1]

PARTICIPATION


PARTY_PROXY

+participation

0..*

+l inks

0..*

+items

1..*

+party

1..1

+archetype_detai ls

0..1

Use ofCIMI-CLUSTER.laboratory_test_observable

CLUSTER modelling patternsFinding

Finding

Finding Group Finding Item


Laboratory Test Result Item Reference Range

CLUSTER

CIMI-CLUSTER.laboratory_test_result_groupCLUSTER

CIMI-CLUSTER.laboratory_test_result_itemCLUSTER

CIMI-CLUSTER.laboratory_test_result_itemCLUSTER

Finding Item

CIMI-CLUSTER.reference_rangeCLUSTER

Finding Item

CLUSTER modelling patternsMaterial Entity

Material Entity

Specimen Anatomical Location

CLUSTER

Specimen Collection Site

CIMI-CLUSTER.specimen

CLUSTER

CIMI-CLUSTER.specimen_collection_site

CLUSTER

Anatomical Location

CLUSTER modelling patternsAction

Observe Action

Action

Interpret Action

Approve Action

Report Action

Cancel Action

Author Action

Issue Action

Custodian Action

Laboratory Test Request Action

Receive Action

Collect Action

Requested ActionRequest Action

Encounter Action

CLUSTER

CIMI-CLUSTER.approve_action

CLUSTER

CIMI-CLUSTER.approve_action

CLUSTER

Action

CIMI-CLUSTER.request_action

CLUSTER

Action

CIMI-CLUSTER.laboratory_test_ request_action

CLUSTER

Action

Request Action

CIMI-CLUSTER.collect_action

CLUSTER

Action

Laboratory Results Report (Template)

CIMI-COMPOSITION-TEMPLATE. laboratory_results_report

Full Blood Count

CIMI-ENTRY.complete_blood_count

• Modular for reusability• Composable for meeting use-cases• Pattern-based for consistency• Maximal for completeness• Logical for implementation in multiple formats• Constraint-based to allow specialisation• Extensible for local requirements• Terminology-bound for isosemanticity &

interoperability

CIMI’s Modeling Approach

Terminology

Use Cases for Terminology in Models

1. Management and quality control of model librariesa) Searching model libraries (e.g. Find all archetypes with a meaning << Observable Entity)

b) Identifying semantic overlap between models (e.g. 2 models that contain a cluster whose elements have the same or similar meanings)

c) Inconsistency of model interdependencies (e.g. the meaning of a constrained archetype is not subsumed by the meaning of the base archetype)

2. Transforming between isosemantic representations of the model: botha) Different levels of precoordination (e.g. ‘Left leg’ versus ‘Leg’ + Laterality= “Left’)

b) Different representation models (e.g. All ENTRYs with meaning << |Observable entity| to be mapped to a HL7 v3 Observation)

3. Querying data instances of models (including clinical decision support) which use different representations – for example:a) Different level of precoordiation versus structure (e.g. ‘Left leg’ versus ‘Leg’ + Laterality=

“Left’)

b) Different modeling design choices (e.g. Representing a medication’s Indication as a data element, versus an ‘indication’ link to a Diagnosis archetype)

c) Subsumption testing of values4. Supporting data validation and semantic interoperability (e.g. Exchanging data

between systems which use different native information structures)

1. Standard (reproducible) way of doing terminology bindings2. The ability to represent the valid set of values for a given coded element.3. The ability to state the association between the intended interpretation of

nodes in the model and concepts in the terminology4. Terminology bindings that are agnostic as to whether nodes are

connected using a hierarchy or using links.5. Terminology bindings that allow the values to be represented in a way

that is agnostic to the degree of precoordination versus structure.6. Terminology bindings that enable the transformation between isosemantic

representations of the same model7. Terminology bindings that allow consistency to be checked within models,

and between models related by specialisation or used to fill slots (using an underlying ontology).

8. Support for semantic node labelling.

Requirements for using Terminology in Models

• Search for: – An archetype whose meaning (without context) is subsumed by ‘Cardiovascular Observable’.

• Validate archetype specialisations:– To ensure that there is a valid relationship between the meanings of the base and the

constrained archetypes – for example:o Not valid: ‘Pulse rate’ (meaning = |pulse finding|) based on ‘Heart rate’ (meaning = |heart

rate|) Meaning from different hierarchieso Valid: ‘Pulse rate’ (meaning = |pulse|) based on ‘Heart rate’ (meaning = |heart rate|)

Meaning of constrained archetype subsumed by meaning of base archetypeo Valid??: ‘Family history of diagnosis’ based on ‘Diagnosis’ archetype Is this

valid, or not? (N.B.: Participation could change)• Validate archetype slot fillers:

– To ensure that the meaning of the slot and the meaning of the archetype that fills it are consistent – for example:o Valid: Using a ‘Problem diagnosis’ archetype (meaning = |clinical finding|) to fill a

‘Cardiovascular problem/diagnosis’ slot (meaning = |cardiovascular finding|).o Using a ‘Problem diagnosis’ archetype to fill the following slots in a discharge summary:

‘Family history’, ‘Past history’, ‘Current problem/diagnosis’, or ‘Problems’ o Using a ‘Medication’ archetype to fill the following slots in a discharge summary :

‘Ceased medication’, ‘Current medication’, or ‘Past Medication’

Management and Quality Control of Model Libraries Example Scenarios

• The meaning of each node is separated into 3 parts: verb, noun, modifier– Relationship: The relationship from the parent node to this node– Object: The ‘class’ of things defined by this node’s values– Modifier: Subject-relationship, temporal and procedure/finding context;

State/Certainty/Negation; Mood code• Note: ‘Subject’ of ‘Subject-rel-object’ triple is the parent node

Terminology Binding Approach

MeaningValue Set

Relationship Object Modifier(Linkage concept)

Pharm/biol product

(Context values) -

(Linkage concept)

Pharm/biol product

(Context values)

Medication Ref_Set

Has active ingredient Substance (Context

values)Substance

Ref_Set

Has basis of strength

substanceSubstance (Context

values)Substance

Ref_Set

Has strength Measurement Finding

(Context values) -

Has dose form

Drug dose form

(Context values)

Dose_Form Ref_Set

Has indication Clinical Finding

(Context values)

Indication Ref_Set

CIMI Terminology Binding Approach

Cluster:

Element:

Element:

Medication

Active ingredient

Element: Dose form

Strength

STRUCTURE TERMINOLOGYBINDING

Medication Name

Element:

IndicationElement:

Element:Basis of Strength

MeaningValue Set


Methotrexate Product

(Context values) -

(Linkage concept)

Methotrexate Product

(Context values)

MethotrexateRef_Set


values)Substance

Ref_Set



values)Substance

Ref_Set


(Context values) -

Has dose form

Drug dose form

(Context values)

Dose_Form Ref_Set

Has indication Clinical Finding

(Context values)

Methotrexate Indications

Ref_Set

Constraining archetype meaning (Object)

Cluster:

Element:

Element:

Methotrexate Medication

Active ingredient

Element: Dose form

Strength


Medication Name

Element:

IndicationElement:


MeaningValue Set


Pharm/Biol Product

(Context values) -

(Linkage concept)

Pharm/Biol Product

(Context values)

Medication Ref_Set


values)Substance

Ref_Set



values)Substance

Ref_Set


(Context values) -

Has dose form

Drug dose form

(Context values)

Dose_Form Ref_Set

Has primary indication

Clinical Finding

(Context values)

Indication Ref_Set

Constraining archetypes (Relationship)

Cluster:

Element:

Element:

Medication with Prim Ind

Active ingredient

Element: Dose form

Strength


Medication name

Element:

Primary Indication

Element:


MeaningValue Set

Relationship Object Modifier

(Linkage concept)

Clinical Finding

(Context values) -

(Linkage concept)

Clinical Finding

(Context values)

Diagnosis Ref_Set

Time aspect Date of onset (Context values) -

Time aspect Date of diagnosis

(Context values) -

Finding context

Finding context value

(Context values)

Clinical Status Ref_Set

Has comment Clinical Finding

(Context values) -

Example: Diagnosis

Cluster:

Element:

Element:

Diagnosis

Onset datetime

Element: Clinical status

Diagnosis datetime


Diagnosis name

Element:

CommentsElement:

MeaningValue Set


(Linkage concept)

Clinical Finding

(Context values) -

MeaningValue Set


Has primary diagnosis

Clinical Finding

(Context values) -

Example: Slot filling (Primary diagnosis)

Cluster:

Element:

Diagnosis

Onset datetime

Diagnosis datetime


Diagnosis name

Element:

Cluster:

Cluster:

Discharge Summary

Primary diagnosis

Medical record number

Element:

MeaningValue Set


(Linkage concept)

Clinical Finding

(Context values) -

MeaningValue Set


Has diagnosis Clinical Finding

Family history (Person in family of subject)

-

Example: Slot filling (Family History)

Cluster:

Element:

Diagnosis

Onset datetime

Diagnosis datetime


Diagnosis name

Element:

Cluster:

Cluster:

Discharge Summary

Family history


Element:

MeaningValue Set


(Linkage concept)

Clinical Finding

(Context values) -

MeaningValue Set


Has secondary disease Disease (Context

values) -

Example: Slot filling (Secondary Disease)

Cluster:

Element:

Diagnosis

Onset datetime

Diagnosis datetime


Diagnosis name

Element:

Cluster:

Cluster:

Discharge Summary

Secondary disease


Element:

MeaningRules Value

SetRelationship Object Modifier

(Linkage concept)

Pharm / biologic product

(Context values) -

MeaningRules Value

SetRelationship Object Modifier

AdministerPharm / biologic product

CeasedCeased medic-ations.Status =

“Ceased”-

Example: Slot Filling (Ceased Medications)

Medication

Active ingredient

Strength


Medication name

Discharge Summary

Ceased medications


Future work & references

• Develop CIMI Modelling Style Guide• Demographics:

– Finalise CIMI Demographics RM & Party Models• Lab Results Report:

– Finish terminology bindings for Lab Results Report– Create Lab Results specialisations (e.g. CBC)– Create Lab Results Report instance examples

• Implementation:– Create ADL & Implementation artefacts (FHIR etc)

• Other models: Immunizations, Temperature

Future Work

• CIMI Web Page– http://informatics.mayo.edu/CIMI

• Google doc repository– http://content.clinicalmodels.org

• Google groups email list (cimi-modelling-taskforce)– http://groups.google.com/group/cimi-modelling-taskforce?hl=

en-GB• Issue tracking (github)

– https://github.com/clinicalmodels/cimi/

Online References

http://informatics.mayo.edu/CIMI

http://content.clinicalmodels.org/

http://groups.google.com/group/cimi-modelling-taskforce?hl=en-GB

http://groups.google.com/group/cimi-modelling-taskforce?hl=en-GB

https://github.com/clinicalmodels/cimi/issues?page=1&state=open

• Volunteer time – Limited time resources• Tooling:

– Urgently need tooling to generate ADL– Need tooling for model display and validation– Need terminology tooling for CIMI value sets– Need repository for sharing models

• Model review process:– Need formal model review processes and governance

Issues for Discussion

Questions

Documents

Modelling Taskforce Report