Knowledge-based best of breed approach for automated detection of clinical events based on German free text digital hospital discharge letters

OBJECTIVES: The secondary use of medical data contained in electronic medical records, such as hospital discharge letters, is a valuable resource for the improvement of clinical care (e.g. in terms of medication safety) or for research purposes. However, the automated processing and analysis of medical free text still poses a huge challenge to available natural language processing (NLP) systems. The aim of this study was to implement a knowledge-based best of breed approach, combining a terminology server with integrated ontology, a NLP pipeline and a rules engine. METHODS: We tested the performance of this approach in a use case. The clinical event of interest was the particular drug-disease interaction "proton-pump inhibitor [PPI] use and osteoporosis". Cases were to be identified based on free text digital discharge letters as source of information. Automated detection was validated against a gold standard. RESULTS: Precision of recognition of osteoporosis was 94.19%, and recall was 97.45%. PPIs were detected with 100% precision and 97.97% recall. The F-score for the detection of the given drug-disease-interaction was 96,13%. CONCLUSION: We could show that our approach of combining a NLP pipeline, a terminology server, and a rules engine for the purpose of automated detection of clinical events such as drug-disease interactions from free text digital hospital discharge letters was effective. There is huge potential for the implementation in clinical and research contexts, as this approach enables analyses of very high numbers of medical free text documents within a short time period

Adding HL7 version 3 data types to PostgreSQL

The HL7 standard is widely used to exchange medical information electronically. As a part of the standard, HL7 defines scalar communication data types like physical quantity, point in time and concept descriptor but also complex types such as interval types, collection types and probabilistic types. Typical HL7 applications will store their communications in a database, resulting in a translation from HL7 concepts and types into database types. Since the data types were not designed to be implemented in a relational database server, this transition is cumbersome and fraught with programmer error. The purpose of this paper is two fold. First we analyze the HL7 version 3 data type definitions and define a number of conditions that must be met, for the data type to be suitable for implementation in a relational database. As a result of this analysis we describe a number of possible improvements in the HL7 specification. Second we describe an implementation in the PostgreSQL database server and show that the database server can effectively execute scientific calculations with units of measure, supports a large number of operations on time points and intervals, and can perform operations that are akin to a medical terminology server. Experiments on synthetic data show that the user defined types perform better than an implementation that uses only standard data types from the database server.Comment: 12 pages, 9 figures, 6 table

User evaluation of a pilot terminologies server for a distributed multi-scheme environment

The present paper reports on a user-centred evaluation of a pilot terminology service developed as part of the High Level Thesaurus (HILT) project at the Centre for Digital Library Research (CDLR) in the University of Strathclyde in Glasgow. The pilot terminology service was developed as an experimental platform to investigate issues relating to mapping between various subject schemes, namely Dewey Decimal Classification (DDC), Library of Congress Subject Headings (LCSH), the Unesco thesaurus, and the MeSH thesaurus, in order to cater for cross-browsing and cross-searching across distributed digital collections and services. The aim of the evaluation reported here was to investigate users' thought processes, perceptions, and attitudes towards the pilot terminology service and to identify user requirements for developing a full-blown pilot terminology service

Multiple terminologies : an obstacle to information retrieval

An issue currently at the forefront of digital library research is the prevalence of disparate terminologies and the associated limitations imposed on user searching. It is thought that semantic interoperability is achievable by improving the compatibility between terminologies and classification schemes, enabling users to search multiple resources simultaneously and improve retrieval effectiveness through the use of associated terms drawn from several schemes. This article considers the terminology issue before outlining various proposed methods of tackling it, with a particular focus on terminology mapping

Challenges and issues in terminology mapping : a digital library perspective

In light of information retrieval problems caused by the use of different subject schemes, this paper provides an overview of the terminology problem within the digital library field. Various proposed solutions are outlined and issues within one approach - terminology mapping are highlighted.Desk-based review of existing research. Findings - Discusses benefits of the mapping approach, which include improved retrieval effectiveness for users and an opportunity to overcome problems associated with the use of multilingual schemes. Also describes various drawbacks such as the labour intensive nature and expense of such an approach, the different levels of granularity in existing schemes, and the high maintenance requirements due to scheme updates, and not least the nature of user terminology. General review of mapping techniques as a potential solution to the terminology problem

Terminology server for improved resource discovery: analysis of model and functions

This paper considers the potential to improve distributed information retrieval via a terminologies server. The restriction upon effective resource discovery caused by the use of disparate terminologies across services and collections is outlined, before considering a DDC spine based approach involving inter-scheme mapping as a possible solution. The developing HILT model is discussed alongside other existing models and alternative approaches to solving the terminologies problem. Results from the current HILT pilot are presented to illustrate functionality and suggestions are made for further research and development

Analysis of equivalence mapping for terminology services

This paper assesses the range of equivalence or mapping types required to facilitate interoperability in the context of a distributed terminology server. A detailed set of mapping types were examined, with a view to determining their validity for characterizing relationships between mappings from selected terminologies (AAT, LCSH, MeSH, and UNESCO) to the Dewey Decimal Classification (DDC) scheme. It was hypothesized that the detailed set of 19 match types proposed by Chaplan in 1995 is unnecessary in this context and that they could be reduced to a less detailed conceptually-based set. Results from an extensive mapping exercise support the main hypothesis and a generic suite of match types are proposed, although doubt remains over the current adequacy of the developing Simple Knowledge Organization System (SKOS) Core Mapping Vocabulary Specification (MVS) for inter-terminology mapping

Formal nursing terminology systems: a means to an end

In response to the need to support diverse and complex information requirements, nursing has developed a number of different terminology systems. The two main kinds of systems that have emerged are enumerative systems and combinatorial systems, although some systems have characteristics of both approaches. Differences in the structure and content of terminology systems, while useful at a local level, prevent effective wider communication, information sharing, integration of record systems, and comparison of nursing elements of healthcare information at a more global level. Formal nursing terminology systems present an alternative approach. This paper describes a number of recent initiatives and explains how these emerging approaches may help to augment existing nursing terminology systems and overcome their limitations through mediation. The development of formal nursing terminology systems is not an end in itself and there remains a great deal of work to be done before success can be claimed. This paper presents an overview of the key issues outstanding and provides recommendations for a way forward

HILT IV : subject interoperability through building and embedding pilot terminology web services

A report of work carried out within the JISC-funded HILT Phase IV project, the paper looks at the project's context against the background of other recent and ongoing terminologies work, describes its outcome and conclusions, including technical outcomes and terminological characteristics, and considers possible future research and development directions. The Phase IV project has taken HILT to the point where the launch of an operational support service in the area of subject interoperability is a feasible option and where both investigation of specific needs in this area and practical collaborative work are sensible and feasible next steps. Moving forward requires detailed work, not only on terminology interoperability and associated service delivery issues, but also on service and end user needs and engagement, service sustainability issues, and the practicalities of interworking with other terminology services and projects in UK, Europe, and global contexts