1. CIMI Terminology Binding Dr Linda Bird 13 th April 2013

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

3. USE CASES AND REQUIREMENTS

4. Use Cases for Terminology in Models 1.Management and quality control of model libraries a)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: both a)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 values 4.Supporting data validation and semantic interoperability (e.g. Exchanging data between systems which use different native information structures)

5. 1.Standard (reproducible) way of doing terminology bindings 2.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 terminology 4.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 model 7.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

6. 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 hierarchies o Valid: ‘Pulse rate’ (meaning = |pulse|) based on ‘Heart rate’ (meaning = |heart rate|) Meaning of constrained archetype subsumed by meaning of base archetype o 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

7. PROPOSED APPROACH

8. 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

9. Meaning Value Set Relationship ObjectModifier (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 substance Substance (Context values) Substance Ref_Set Has strength Measuremen t 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: Medication Active ingredient Element: Dose form Strength STRUCTURE TERMINOLOGYBINDING Medication Name Element: Indication Element: Basis of Strength

10. Meaning Value Set Relationship ObjectModifier (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 substance Substance (Context values) Substance Ref_Set Has strength Measuremen t 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: Oral Medication Active ingredient Element: Dose form Strength STRUCTURE TERMINOLOGYBINDING Medication Name Element: Indication Element: Basis of Strength

11. Meaning Value Set Relationship ObjectModifier (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 substance Substance (Context values) Substance Ref_Set Has strength Measurem ent 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: Medication with Primary Indication Active ingredient Element: Dose form Strength STRUCTURE TERMINOLOGYBINDING Medication Name Element: Indication Element: Basis of Strength

12. Meaning Value Set Relationship ObjectModifier (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 substance Substance (Context values) Substance Ref_Set Has strength Measuremen t 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: Current Medication Active ingredient Element: Dose form Strength STRUCTURE TERMINOLOGYBINDING Medication Name Element: Indication Element: Basis of Strength

13. Meaning Value Set Relationship ObjectModifier Has diagnosis Clinical Finding (Context values) - Meaning Value Set Relationship ObjectModifier Has primary diagnosis Clinical Finding (Context values) - Filling Archetype Slots Cluster: Element: Diagnosis Onset datetime Element: Clinical status Diagnosis datetime STRUCTURE TERMINOLOGY BINDING Diagnosis name Element: Comments Element: Composition Cluster: Discharge Summary Primary diagnosis Medical record number Element:

14. Meaning Value Set Relationship ObjectModifier Has diagnosis Clinical finding (Context values) - Meaning Value Set Relationship ObjectModifier Has primary diagnosis Clinical finding Family member - Filling Archetype Slots Cluster: Element: Diagnosis Onset datetime Element: Clinical status Diagnosis datetime STRUCTURE TERMINOLOGY BINDING Diagnosis name Element: Comments Element: Composition Cluster: Discharge Summary Family history Medical record number Element:

15. EXAMPLE LABORATORY RESULTS MODEL BINDINGS

16. Laboratory Test Request Summary Clinical Entry Observation Request Request Clinical Activity ENTRY constrains

17. Clinical Entry

18. Clinical Entry & Clinical Activity constrains

19. Clinical Activity & Request constrains

20. Request & Observation Request constrains

21. Observation Request & Laboratory Test Request Summary constrains

22. TERMINOLOGY REFERENCE SETS

23. 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.

24. 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.

25. CIMI Reference Sets IdNameTerminologyModelModel attribute/element 1 CIMI_action_type_refset SNOMED CTCIMI-CLUSTER.actionaction_type 2 CIMI_composition_category_refset CIMI value set (non-clinical)CIMI-RMCOMPOSITION.category 3 CIMI_finding_status_refset SNOMED CT CIMI- CLUSTER.observation_result_item finding_status 4 CIMI_formalism_refset CIMI value set (non-clinical)CIMI-RMPARSABLE.formalism 5 CIMI_identifier_type_refset SNOMED CTCIMI-RMIDENTIFIER.type 6 CIMI_language_refset ISO-639-1/2 [+ ISO-3166-1] (e.g. 'en', 'en-GB', 'en-US')CIMI-RM COMPOSITION.language ENTRY.language TEXT.language 7 CIMI_link_meaning_refset SNOMED CTCIMI-RMLINK.meaning 8 CIMI_link_type_refset SNOMED CTCIMI-RMLINK.type 9 CIMI_mapping_purpose_refset CIMI-RMTERM_MAPPING.purpose 10 CIMI_media_type_refset IANA media types (e.g. 'html', 'csv', 'jpeg')CIMI-RMMULTIMEDIA.media_type 11 CIMI_null_flavour_refset HL7 v3 Null flavorsCIMI-RMELEMENT.null_flavor 12 CIMI_observation_interpretation_category _refset SNOMED CT CIMI-ENTRY.observation CIMI- CLUSTER.observation_result_item results/interpretation_category interpretation_category 13 CIMI_observation_result_refset SNOMED CT CIMI- CLUSTER.observation_result_item name 14 CIMI_observation_result_group_refset SNOMED CTCIMI-ENTRY.observationresults/result_group_name 15 CIMI_participation_function_refset SNOMED CTCIMI-RMPARTICIPATION.function 16 CIMI_participation_mode_refset CIMI value set (non-clinical)CIMI-RMPARTICIPATION.mode 17 CIMI_party_relationship_refset SNOMED CTCIMI-RMPARTY_RELATED.relationship 18 CIMI_procedure_status_refset SNOMED CT CIMI-CLUSTER.action_information CIMI-ENTRY.procedure CIMI-ENTRY.observation action/action_status procedure/status observable/status 19 CIMI_proportion_type_refset CIMI value set (non-clinical)CIMI-RMPROPORTION.type 20 CIMI_structure_type_refset CIMI value set (non-clinical)CIMI-RMCLUSTER.structure_type 21 CIMI_symbol_refset CIMI value set (non-clinical)CIMI-RMORDINAL.symbol 22 CIMI_territory_refset CIMI value set (non-clinical)CIMI-RMCOMPOSITION.territory 23 CIMI_units_refset SNOMED CTCIMI-RMQUANTITY.units 24 CIMI_units_duration_refset SNOMED CTCIMI-RMDURATION.units

26. CIMI_link_meaning_refset

27. ARCHETYPE OBJECT MODEL SUPPORT

28. AOM 1.5 Ontology

29. To define the ‘relationship-object-modifier’ triplet as an allowable binding statement. Option 1 – Make binding triple explicit ontology term_bindings = object = modifier = > ["/data[cimi-CLUSTER.report_action] "] = object = modifier = > >

30. Use SNOMED CT Compositional Grammar inline. Option 2 – Use SNOMED CT CG ontology term_bindings =

31. FUTURE WORK

32. 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

33. QUESTIONS