Mikael Nyström

Integration of Tools for Binding Archetypes to SNOMED CT

BackgroundThe Archetype formalism and the associated Archetype Definition Language have been proposed as an ISO standard for specifying models of components of electronic healthcare records as a means of achieving interoperability between clinical systems. This paper presents an archetype editor with support for manual or semi-automatic creation of bindings between archetypes and terminology systems.MethodsLexical and semantic methods are applied in order to obtain automatic mapping suggestions. Information visualisation methods are also used to assist the user in exploration and selection of mappings.ResultsAn integrated tool for archetype authoring, semi-automatic SNOMED CT terminology binding assistance and terminology visualization was created and released as open source.ConclusionFinding the right terms to bind is a difficult task but the effort to achieve terminology bindings may be reduced with the help of the described approach. The methods and tools presented are general, but here only bindings between SNOMED CT and archetypes based on the openEHR reference model are presented in detail.

Enriching a primary health care version of ICD-10 using SNOMED CT mapping

BackgroundIn order to satisfy different needs, medical terminology systems must have richer structures. This study examines whether a Swedish primary health care version of the mono-hierarchical ICD-10 (KSH97-P) may obtain a richer structure using category and chapter mappings from KSH97-P to SNOMED CT and SNOMED CTs structure. Manually-built mappings from KSH97-Ps categories and chapters to SNOMED CTs concepts are used as a starting point.ResultsThe mappings are manually evaluated using computer-produced information and a small number of mappings are updated. A new and poly-hierarchical chapter division of KSH97-Ps categories has been created using the category and chapter mappings and SNOMED CTs generic structure. In the new chapter division, most categories are included in their original chapters. A considerable number of concepts are included in other chapters than their original chapters. Most of these inclusions can be explained by ICD-10s design. KSH97-Ps categories are also extended with attributes using the category mappings and SNOMED CTs defining attribute relationships. About three-fourths of all concepts receive an attribute of type Finding site and about half of all concepts receive an attribute of type Associated morphology. Other types of attributes are less common.ConclusionsIt is possible to use mappings from KSH97-P to SNOMED CT and SNOMED CTs structure to enrich KSH97-Ps mono-hierarchical structure with a poly-hierarchical chapter division and attributes of type Finding site and Associated morphology. The final mappings are available as additional files for this paper.

Applying representational state transfer (REST) architecture to archetype-based electronic health record systems

BackgroundThe openEHR project and the closely related ISO 13606 standard have defined structures supporting the content of Electronic Health Records (EHRs). However, there is not yet any finalized openEHR specification of a service interface to aid application developers in creating, accessing, and storing the EHR content.The aim of this paper is to explore how the Representational State Transfer (REST) architectural style can be used as a basis for a platform-independent, HTTP-based openEHR service interface. Associated benefits and tradeoffs of such a design are also explored.ResultsThe main contribution is the formalization of the openEHR storage, retrieval, and version-handling semantics and related services into an implementable HTTP-based service interface. The modular design makes it possible to prototype, test, replicate, distribute, cache, and load-balance the system using ordinary web technology. Other contributions are approaches to query and retrieval of the EHR content that takes caching, logging, and distribution into account. Triggering on EHR change events is also explored.A final contribution is an open source openEHR implementation using the above-mentioned approaches to create LiU EEE, an educational EHR environment intended to help newcomers and developers experiment with and learn about the archetype-based EHR approach and enable rapid prototyping.ConclusionsUsing REST addressed many architectural concerns in a successful way, but an additional messaging component was needed to address some architectural aspects. Many of our approaches are likely of value to other archetype-based EHR implementations and may contribute to associated service model specifications.

Creating a medical English-Swedish dictionary using interactive word alignment

BackgroundThis paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish.MethodsThe medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates.ResultsA dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages.ConclusionIn three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems.

Creating a medical dictionary using word alignment: the influence of sources and resources.

BackgroundAutomatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality.MethodsWe automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary.ResultsThe results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English-Swedish dictionary contains 24,000 term pairs in base forms.ConclusionMore resources give better results in the automatic word alignment, but some resources only give small improvements. The most important type of resource is training and the most general resources were generated from ICD-10.

User-directed coordination in SNOMED CT

The possibility of post-coordination of SNOMED CT concepts, especially by clinical users, is both an asset and a challenge for SNOMED CT implementation. To get insight in the applicability of post-coordination, we analyzed scenarios for user-directed coordination that are described in the documentation of SNOMED CT. The analyses were based on experiences from previous and ongoing research and implementation work, including national mapping projects, and investigations on collection of data for multiple uses. These scenarios show various usability and representation problems: high number of relationships for refinement and qualification, improper options for refinement, incorrect formal definitions, and lack of support for applying editorial rules. Improved user-directed coordination in SNOMED CT in real practice requires advanced sanctioning, increased consistency of definitions of concepts in SNOMED CT, and real-time analysis of the post-coordinate expression.

Coding of procedures documented by general practitioners in Swedish primary care-an explorative study using two procedure coding systems

BackgroundProcedures documented by general practitioners in primary care have not been studied in relation to procedure coding systems. We aimed to describe procedures documented by Swedish general practitioners in electronic patient records and to compare them to the Swedish Classification of Health Interventions (KVÅ) and SNOMED CT.MethodsProcedures in 200 record entries were identified, coded, assessed in relation to two procedure coding systems and analysed.Results417 procedures found in the 200 electronic patient record entries were coded with 36 different Classification of Health Interventions categories and 148 different SNOMED CT concepts. 22.8% of the procedures could not be coded with any Classification of Health Interventions category and 4.3% could not be coded with any SNOMED CT concept. 206 procedure-concept/category pairs were assessed as a complete match in SNOMED CT compared to 10 in the Classification of Health Interventions.ConclusionsProcedures documented by general practitioners were present in nearly all electronic patient record entries. Almost all procedures could be coded using SNOMED CT.Classification of Health Interventions covered the procedures to a lesser extent and with a much lower degree of concordance. SNOMED CT is a more flexible terminology system that can be used for different purposes for procedure coding in primary care.

Can We Quantify Domainhood? Exploring Measures to Assess Domain-Specificity in Web Corpora

Web corpora are a cornerstone of modern Language Technology. Corpora built from the web are convenient because their creation is fast and inexpensive. Several studies have been carried out to assess the representativeness of general-purpose web corpora by comparing them to traditional corpora. Less attention has been paid to assess the representativeness of specialized or domain-specific web corpora. In this paper, we focus on the assessment of domain representativeness of web corpora and we claim that it is possible to assess the degree of domain-specificity, or domainhood, of web corpora. We present a case study where we explore the effectiveness of different measures - namely the Mann-Withney-Wilcoxon Test, Kendall correlation coefficient, Kullback–Leibler divergence, log-likelihood and burstiness - to gauge domainhood. Our findings indicate that burstiness is the most suitable measure to single out domain-specific words from a specialized corpus and to allow for the quantification of domainhood.

A Web Corpus for eCare: Collection, Lay Annotation and Learning -First Results-

In this position paper, we put forward two claims: 1) it is possible to design a dynamic and extensible corpus without running the risk of getting into scalability problems; 2) it is possible to de ...