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A Study of Semantic Proximity between Archetype Terms based on SNOMED CT Relationships
 

A Study of Semantic Proximity between Archetype Terms based on SNOMED CT Relationships

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The aim of OpenEHR archetypes is sharing clinical data in a unambiguous and ...

The aim of OpenEHR archetypes is sharing clinical data in a unambiguous and
accurate way. Standard terminologies, such as SNOMED CT, provide an appro-
priate method of expressing unambiguous and interoperable clinical data terms.
However, nowadays bindings to terminologies are infrequent in the archetypes,
probably because manual mapping requires a lot of human resources.
The work has analyzed clinical archetypes and has detected a high degree of
semantic proximity between their terms, using the SNOMED CT relationships
as a reference. Moreover, taking advantage of this, an automated method to
map archetype terms to SNOMED CT concepts has been proposed. The method
exploits the SNOMED CT relationships to limit the searches to relevant portions
of the terminology. This contribution clearly improves mapping results.
This research shows that it is possible to automatically map archetype terms
to a standard terminology with a high precision and recall, with the help of
appropriate contextual and semantic information of both models.

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    A Study of Semantic Proximity between Archetype Terms based on SNOMED CT Relationships A Study of Semantic Proximity between Archetype Terms based on SNOMED CT Relationships Presentation Transcript

    • Background Objectives Semantic proximity in archetypes Mapping archetypes to SNOMED. A Study of Semantic Proximity between Archetype Terms based on SNOMED CT Relationships. J.L.Allones, D.Penas, M.Taboada, D.Martinez and S.Tellado KEAM Research Group . . . . . .J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Objectives Semantic proximity in archetypes Mapping archetypes to SNOMED. Outline . 1 Background OpenEHR archetypes SNOMED CT Related Work . 2 Objectives . 3 Semantic proximity in archetypes Dataset Methods Results Conclusion . 4 Mapping archetypes to SNOMED Methods Evaluation Results Discussion . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. Outline . 1 Background OpenEHR archetypes SNOMED CT Related Work . 2 Objectives . 3 Semantic proximity in archetypes Dataset Methods Results Conclusion . 4 Mapping archetypes to SNOMED Methods Evaluation Results Discussion . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. OpenEHR archetypes . What is openEHR? . Open standard specification that describes the management, storage and exchange of clinical data in EHR. . . What are the archetypes? . OpenEHR defines clinical data models called archetypes. They model the clinical information required to record particular clinical statements, such as tobacco use and exposure. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. OpenEHR archetypes Extract of the archetype tobacco: . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. OpenEHR archetypes . Current status of archetypes . Important institutions have participated in the development of archetypes. Problem: Archetypes hardly contain mappings to standard concepts . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. OpenEHR archetypes: Need for clinical terminologies . Terminologies are required: To capture, use and transfer clinical data in a standard form. To reuse information collected in the course of patient care. Challenge of health informatics: . To integrate archetypes and terminologies. . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. SNOMED CT . SNOMED CT is the best positioned terminology to semantically annotate archetypes because it is an international standard which provides a consistent terminology across all health care domains. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. SNOMED CT . Features: Over 300,000 medical concepts. Concepts can have several descriptions and semantic relationships to other concepts. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. SNOMED CT . IS A relationships are also known as ”Supertype - Subtype relationships”. IS A relationships are the basis of SNOMED CT’s hierarchies. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. SNOMED CT . Attribute relationships associate two concepts speci- fying a defining characteristic of one of the concepts. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED.Need for automated mapping. SNOMED is a huge terminology ↓ Manual annotation of archetypes with SNOMED concepts is very time-consuming. ↓ Automated mapping methods are needed.. . . . . . .J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. Related Work . Some studies have used lexical and linguistic techniques to compare the strings of archetype fragments and SNOMED CT concepts. The works have not achieved optimum results: They map correctly about 60% of archetype fragments. They obtain too many candidate concepts for each fragment (many of them are not relevant). . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. Related Work . Difficulties in automated mapping . . 1 Modelling archetypes separately from SNOMED leads to differences between them: disparity in documentation granularity or naming differences . Example of naming differences: . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. Related Work . Difficulties in automated mapping . . 2 Some archetype terms have not been explicitly modelled in the archetypes. . Example: . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background OpenEHR archetypes Objectives SNOMED CT Semantic proximity in archetypes Related Work Mapping archetypes to SNOMED. There are plenty of situations in which archetype clinical information is semantically related Similarities between the structure of the archetypes and the network of SNOMED relationships ↓. This may help in the automated mapping . . . . . .J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Objectives Semantic proximity in archetypes Mapping archetypes to SNOMED. Outline . 1 Background OpenEHR archetypes SNOMED CT Related Work . 2 Objectives . 3 Semantic proximity in archetypes Dataset Methods Results Conclusion . 4 Mapping archetypes to SNOMED Methods Evaluation Results Discussion . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Objectives Semantic proximity in archetypes Mapping archetypes to SNOMED. Objectives . . 1 To understand better how archetype clinical information is semantically related. . To evaluate whether a combination of context 2 and structure-based techniques with lexical and linguistic techniques can improve the automated mapping of archetypes. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Outline . 1 Background OpenEHR archetypes SNOMED CT Related Work . 2 Objectives . 3 Semantic proximity in archetypes Dataset Methods Results Conclusion . 4 Mapping archetypes to SNOMED Methods Evaluation Results Discussion . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Studying semantic proximity between archetype terms . We checked the frequency and type of semantic relationships between data fragments of 25 archetypes. SNOMED relationships are the reference. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Dataset: 25 Observation archetpes . 25 OBSERVATION archetypes of the NHS repository. information about the condi- These archetypes record tion of patients, such as the measurement of heart rate and tobacco use. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Parsing archetypes . A parser was used to preserve data fragments with clinical meaning. Parser gets a dependency tree of data fragments for each archetype. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Parsing archetypes: Types of data fragments in archetypes . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Creating manual mappings . SNOMED concepts are required to study semantic proximity. Problem: Bindings to SNOMED concepts are very scarce. We manually created mappings through manual searches. . This process was very tedious and time-consuming. . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Evaluating the semantic proximity . We checked if the concepts mapped to these archetype fragments are linked through hierarchical and logical relationships of the SNOMED terminology. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Results . A high ratio of archetype terms are semantically related: 30% of Element fragments are subtypes of the Root fragment. 80% of Value fragments are connected through hierarchical . relationships to any other Value fragment of the archetype . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Dataset Objectives Methods Semantic proximity in archetypes Results Mapping archetypes to SNOMED Conclusion. Conclusion . A high ratio of archetype terms are semantically related ↓ The network of SNOMED relationships should be exploited during the automated mapping of archetypes. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Outline . 1 Background OpenEHR archetypes SNOMED CT Related Work . 2 Objectives . 3 Semantic proximity in archetypes Dataset Methods Results Conclusion . 4 Mapping archetypes to SNOMED Methods Evaluation Results Discussion . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Automated mapping between archetypes and SNOMED . Several mapping techniques were developed to bind archetype fragments to SNOMED concepts: Lexical techniques Linguistic resource-based techniques Terminological context-based techniques Structure-based techniques . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Lexical techniques . Lexical techniques identify SNOMED concepts and archetype terms with similar names. Both the archetype terms and SNOMED descriptions are nor- malized, including plurals, singulars, case-insensitive, etc. . Example: . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Linguistic resource-based techniques . We used several linguistic resources provided by the UMLS. These resources use a knowledge-intensive approach based on symbolic and natural-language processing, to discover biomed- ical concepts referred in a text. . Example: . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Degree of lexical similarity . Two degrees of lexical similarity: Full or exact match occurs when an archetype terms is exactly the same as some SNOMED CT description after normalization. Partial match occurs when the archetype term is contained in- side some SNOMED CT description. . Example: . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Mapping algorithm . The mapping algorithm consists of three steps: . Exact Match in entire SNOMED 1 . Partial Match in SNOMED contexts 2 . Structural similarity 3 . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. First step of Mapping: Exact Match in entire SNOMED . Lexical and linguistic techniques are used to discover exact or almost exact correspondeces between all the SNOMED concepts and archetype fragments . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Second step of Mapping: Partial Match in SNOMED contexts . SNOMED contexts are extracted from the concepts obtained in the previous step. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Second step of Mapping: Partial Match in SNOMED contexts . Lexical and linguistic techniques are used to discover partial and approximate correspondeces in the extracted contexts. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Third step of Mapping: Structural similarity . Structure-based techniques identify structural similarities between the tree structure of archetypes and the network of SNOMED rela- tionships → Equivalent entities with different names can be mapped . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Evaluation . Our mapping algorithm was applied to 25 archetypes. The evaluation entailed the automated revision of each mapping generated by the method against the manual mappings that we had created for the study. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Results . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Results: Comparison with other approaches . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Discussion . Lessons learned in the work . Objetive 1: To understand better how archetype clinical infor- mation is semantically related. We now know the frequency and type of semantic relationships between data fragments of archetypes. We found that a high ratio of archetype fragments are seman- tically related. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Discussion . Lessons learned in the work . Objetive 2: To evaluate whether a combination of context and structure-based techniques with lexical and linguistic techniques can improve the automated mapping. Context and structure-based techniques are able to exploit SNOMED CT relationships to improve the automated mapping of archetypes. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Future Work . We will test the automatic mapping with different types of archetypes. We will explore ways to use medical knowledge from SNOMED: To facilitate the semi-automatic creation of new archetypes. To recommend extensions in existing archetypes. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Summary . Clinical models, such as archetypes, need to be inte- grated with terminologies to capture, use and transfer clinical data in a standard way. Manual integration is very time-consuming... . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Summary . We propose a novel automated method to link data fragments of archetypes with concepts of medical ter- minologies. Besides conventional name-based techniques, the method exploits the medical knowledge represented in SNOMED to improve the automated mapping and thus reduce human participation in the process. . . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o
    • Background Methods Objectives Evaluation Semantic proximity in archetypes Results Mapping archetypes to SNOMED Discussion. Acknowledgements Thank you for your attention! MEC National research project Gesti´n de Terminolog´ M´dicas o ıas e para Arquetipos TIN2009-14159-C05-05 . . . . . . J.L. Allones, D. Penas, M. Taboada, D. Martinez et al. A Study of Semantic Proximity between Archetype Terms based o