CIMI Terminology BindingDr Linda Bird13th April 2013

Agenda

• Use Cases and Requirements• Proposed Approach• Example Lab Results Bindings• Terminology Reference Sets• Archetype Object Model Support• Future Work

USE CASES AND REQUIREMENTS

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).

Requirements for using Terminology in Models

• Search for: – An archetype whose meaning ( ̶ 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

• 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

PROPOSED APPROACH

• The meaning of each node is separated into 3 parts:– Relationship: The relationship from the parent node to this node– Object: The ‘class’ of things defined by this node’s values– Modifier: The context of the node’s meaning – including Subject-relationship,

temporal, procedure/finding context, negation, state, certainty

• Note: ‘Subject’ of ‘Subject-Relationship-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

Relationship Object Modifier(Linkage concept)

Oral dosage form product

(Context values) -

(Linkage concept)

Oral dosage form product

(Context values)

Oral Medict 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

Oral dosage form

(Context values)

Oral Dose_Form

Ref_Set

Has indication

Clinical Finding

(Context values)

Indication Ref_Set

Specialising Archetype Meaning (Object)

Cluster:

Element:

Element:

Oral Medication

Active ingredient

Element: Dose form

Strength

STRUCTURE TERMINOLOGYBINDING

Medication Name

Element:

IndicationElement:

Element:Basis of Strength

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 primary indication

Clinical Finding

(Context values)

Indication Ref_Set

Specialising Archetype Meaning (Relationship)

Cluster:

Element:

Element:

Medication with Primary

Indication

Active ingredient

Element: Dose form

Strength

STRUCTURE TERMINOLOGYBINDING

Medication Name

Element:

IndicationElement:

Element:Basis of Strength

MeaningValue Set

Relationship Object Modifier(Linkage concept)

Pharm/biol product Current -

(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

Specialising Archetype Meaning (Modifier)

Cluster:

Element:

Element:

Current Medication

Active ingredient

Element: Dose form

Strength

STRUCTURE TERMINOLOGYBINDING

Medication Name

Element:

IndicationElement:

Element:Basis of Strength

MeaningValue Set

Relationship Object Modifier

Has diagnosis Clinical Finding

(Context values) -

MeaningValue Set

Relationship Object Modifier

Has primary diagnosis

Clinical Finding

(Context values) -

Filling Archetype Slots

Cluster:

Element:

Diagnosis

Onset datetime

Diagnosis datetime

STRUCTURE TERMINOLOGYBINDING

Diagnosis name

Element:

Composition

Cluster:

Discharge Summary

Primary diagnosis

Medical record number

Element:

MeaningValue Set

Relationship Object Modifier

Has diagnosis

Clinical finding

(Context values) -

MeaningValue Set

Relationship Object Modifier

Has primary diagnosis

Clinical finding

Family member -

Filling Archetype Slots

Cluster:

Element:

Diagnosis

Onset datetime

Diagnosis datetime

STRUCTURE TERMINOLOGYBINDING

Diagnosis name

Element:

Composition

Cluster:

Discharge Summary

Family history

Medical record number

Element:

EXAMPLE LABORATORY RESULTS MODEL BINDINGS

Laboratory Test Request Summary

Laboratory Test Request

Summary

Clinical Entry

Observation Request

Request

Clinical Activity

ENTRY

constrains

constrains

constrains

constrains

constrains

Clinical Entry

Clinical Entry & Clinical Activity

constrains

Clinical Activity & Request

constrains

Request & Observation Request

constrains

Observation Request & Laboratory Test Request Summary

constrains

TERMINOLOGY REFERENCE SETS

Categories of value sets

1. Clinical value sets • For these we will try to always use SNOMED CT, with the addition

of CIMI extension concepts where required.

2. Non-clinical value sets, with a single authoritative ‘source of truth’  (e.g. IANA media types, country codes) • For these we will take a copy of the value set into our terminology

server, so that the values are available during the authoring process and instance generation.

3. Non-clinical value sets, with no single authoritative ‘source of truth’ (e.g. participation mode) • For these we will provide a maximal set of terms that provides

coverage of all member’s value sets, and include a hierarchy that indicates the relationship between a value and its specialisations.

General Principle

Value sets which may either be represented in the structure or precoordinated in the definition of another clinical concept (e.g. ‘units of measure’ may be used to define the strength of a medication) would be represented using SNOMED CT, to ensure that the concept definitions can be incorporated into SNOMED CT for isosemanticity .

CIMI Reference SetsId Name Terminology Model Model attribute/element1 CIMI_action_type_refset SNOMED CT CIMI-CLUSTER.action action_type2 CIMI_composition_category_refset CIMI value set (non-clinical) CIMI-RM COMPOSITION.category3 CIMI_finding_status_refset SNOMED CT CIMI-

CLUSTER.observation_result_item finding_status4 CIMI_formalism_refset CIMI value set (non-clinical) CIMI-RM PARSABLE.formalism5 CIMI_identifier_type_refset SNOMED CT CIMI-RM IDENTIFIER.type

6 CIMI_language_refsetISO-639-1/2 [+ ISO-3166-1](e.g. 'en', 'en-GB', 'en-US') CIMI-RM

COMPOSITION.languageENTRY.languageTEXT.language

7 CIMI_link_meaning_refset SNOMED CT CIMI-RM LINK.meaning8 CIMI_link_type_refset SNOMED CT CIMI-RM LINK.type9 CIMI_mapping_purpose_refset CIMI-RM TERM_MAPPING.purpose

10 CIMI_media_type_refsetIANA media types

(e.g. 'html', 'csv', 'jpeg') CIMI-RM MULTIMEDIA.media_type

11 CIMI_null_flavour_refset HL7 v3 Null flavors CIMI-RM ELEMENT.null_flavor

12 CIMI_observation_interpretation_category_refset SNOMED CT

CIMI-ENTRY.observationCIMI-

CLUSTER.observation_result_itemresults/interpretation_category

interpretation_category

13 CIMI_observation_result_refset SNOMED CT CIMI-CLUSTER.observation_result_item name

14 CIMI_observation_result_group_refset SNOMED CT CIMI-ENTRY.observation results/result_group_name15 CIMI_participation_function_refset SNOMED CT CIMI-RM PARTICIPATION.function16 CIMI_participation_mode_refset CIMI value set (non-clinical) CIMI-RM PARTICIPATION.mode17 CIMI_party_relationship_refset SNOMED CT CIMI-RM PARTY_RELATED.relationship

18 CIMI_procedure_status_refset SNOMED CTCIMI-CLUSTER.action_information

CIMI-ENTRY.procedureCIMI-ENTRY.observation

action/action_statusprocedure/statusobservable/status

19 CIMI_proportion_type_refset CIMI value set (non-clinical) CIMI-RM PROPORTION.type20 CIMI_structure_type_refset CIMI value set (non-clinical) CIMI-RM CLUSTER.structure_type21 CIMI_symbol_refset CIMI value set (non-clinical) CIMI-RM ORDINAL.symbol22 CIMI_territory_refset CIMI value set (non-clinical) CIMI-RM COMPOSITION.territory23 CIMI_units_refset SNOMED CT CIMI-RM QUANTITY.units24 CIMI_units_duration_refset SNOMED CT CIMI-RM DURATION.units

CIMI_link_meaning_refset

ARCHETYPE OBJECT MODEL SUPPORT

AOM 1.5 Ontology

To define the ‘relationship-object-modifier’ triplet as an allowable binding statement.

Option 1 – Make binding triple explicit

ontology    term_bindings = <        ["/data[cimi-CLUSTER.observe_action] "] = <            relationship = <[SNOMED_CT::5635636|Has related action|]>            object = <[SNOMED_CT::123456|Observation procedure|]>             modifier = <[SNOMED_CT::288529006 |Context values|]>        >        ["/data[cimi-CLUSTER.report_action] "] = <            relationship = <[SNOMED_CT::5635636|Has related action|]>            object = <[SNOMED_CT::243256|Report procedure|]>             modifier = <[SNOMED_CT::288529006 |Context values|]>        >    >

Use SNOMED CT Compositional Grammar inline.

Option 2 – Use SNOMED CT CG

ontology    term_bindings = <        ["/data[cimi-CLUSTER.observe_action]"] = <[SNOMEDCT::{5635636|Has related action|=123456|Observation procedure|:288529006|Context values|]>

FUTURE WORK

Future Work

• Value bindings:– List the full set of reference sets required– Populate these reference sets

• Semantic bindings:– Complete semantic bindings for Model Patterns– Complete semantic bindings for Lab Results Models

• Explore the relationship between the ‘Modifier’ binding and data elements, such as ‘Status’, ‘Certainty’, and ‘Negation flag’.

• Define other rules and principles• Complete Terminology Binding Style Guide

QUESTIONS