cimi terminology binding
DESCRIPTION
CIMI Terminology Binding. Dr Linda Bird 13 th 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. - PowerPoint PPT PresentationTRANSCRIPT
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