Linked data and online classifications to organise mined patterns in patient data

In this paper, we investigate the use of web data resources in medicine, especially through medical classifications made available using the principles of Linked Data, to support the interpretation of patterns mined from patient care trajectories. Interpreting such patterns is naturally a challenge for an analyst, as it requires going through large amounts of results and access to sufficient background knowledge. We employ linked data, especially as exposed through the BioPortal system, to create a navigation structure within the patterns obtained form sequential pattern mining. We show how this approach provides a flexible way to explore data about trajectories of diagnoses and treatments according to different medical classifications

Some Issues on Ontology Integration

The word integration has been used with different meanings in the ontology field. This article aims at clarifying the meaning of the word “integration” and presenting some of the relevant work done in integration. We identify three meanings of ontology “integration”: when building a new ontology reusing (by assembling, extending, specializing or adapting) other ontologies already available; when building an ontology by merging several ontologies into a single one that unifies all of them; when building an application using one or more ontologies. We discuss the different meanings of “integration”, identify the main characteristics of the three different processes and proposethree words to distinguish among those meanings:integration, merge and use

An iconic language for the graphical representation of medical concepts

<p>Abstract</p> <p>Background</p> <p>Many medication errors are encountered in drug prescriptions, which would not occur if practitioners could remember the drug properties. They can refer to drug monographs to find these properties, however drug monographs are long and tedious to read during consultation. We propose a two-step approach for facilitating access to drug monographs. The first step, presented here, is the design of a graphical language, called VCM.</p> <p>Methods</p> <p>The VCM graphical language was designed using a small number of graphical primitives and combinatory rules. VCM was evaluated over 11 volunteer general practitioners to assess if the language is easy to learn, to understand and to use. Evaluators were asked to register their VCM training time, to indicate the meaning of VCM icons and sentences, and to answer clinical questions related to randomly generated drug monograph-like documents, supplied in text or VCM format.</p> <p>Results</p> <p>VCM can represent the various signs, diseases, physiological states, life habits, drugs and tests described in drug monographs. Grammatical rules make it possible to generate many icons by combining a small number of primitives and reusing simple icons to build more complex ones. Icons can be organized into simple sentences to express drug recommendations. Evaluation showed that VCM was learnt in 2 to 7 hours, that physicians understood 89% of the tested VCM icons, and that they answered correctly to 94% of questions using VCM (versus 88% using text, <it>p </it>= 0.003) and 1.8 times faster (<it>p </it>< 0.001).</p> <p>Conclusion</p> <p>VCM can be learnt in a few hours and appears to be easy to read. It can now be used in a second step: the design of graphical interfaces facilitating access to drug monographs. It could also be used for broader applications, including the design of interfaces for consulting other types of medical document or medical data, or, very simply, to enrich medical texts.</p

Application of User Profiling on Ontology Module Extraction for Medical portals

One fit all for approach for searching and ranking discovered knowledge on the Internet does not cater for the diverse variety of users and user groups with different preferences, information needs and priorities. This is of a particular case in the National electronic Library of Infection in the UK (NeLI, www.neli.org.uk) accessed by a number of medical professionals with different preferences and medical information needs. We define personal and group profiles, based on user-specified interests, and develop an ontology module extraction service defining the key area of the infection ontology of a particular relevance to each user group. In this paper we discuss how ontology modularisation can improve the NeLI portal by providing customised alert, recommender service and specialitycustomised browsing tree structure

Structuring an event ontology for disease outbreak detection

<p>Abstract</p> <p>Background</p> <p>This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is designed to support timely detection of disease outbreaks and rapid judgment of their alerting status by 1) bridging a gap between layman's language used in disease outbreak reports and public health experts' deep knowledge, and 2) making multi-lingual information available.</p> <p>Construction and content</p> <p>This event ontology integrates a model of experts' knowledge for disease surveillance, and at the same time sets of linguistic expressions which denote disease-related events, and formal definitions of events. In this ontology, rather general event classes, which are suitable for application to language-oriented tasks such as recognition of event expressions, are placed on the upper-level, and more specific events of the experts' interest are in the lower level. Each class is related to other classes which represent participants of events, and linked with multi-lingual synonym sets and axioms.</p> <p>Conclusions</p> <p>We consider that the design of the event ontology and the methodology introduced in this paper are applicable to other domains which require integration of natural language information and machine support for experts to assess them. The first version of the ontology, with about 40 concepts, will be available in March 2008.</p

Importance of Measuring Sentential Semantic Knowledge Base of a "Free Text" Medical Corpus

At present, the healthcare industry uses codified data mainly for billing purpose. Codified data could be used to improve patient care through decision support and analytical systems. However to reduce medical errors, these systems need access to a wide range of medical data. Unfortunately, a great deal of data is only available in a narrative or free text form, requiring natural language processing (NLP) techniques for their codification. Structuring narrative data and analyzing their underlying meaning from a medical domain requires extensive knowledge acquired through studying the domain empirically. Existing NLP system like MedLEE has a limited ability to analyze free text medical observations and codify data against Unified Medical Language System (UMLS) codes. MedLEE was successful in extracting meaning from relatively simple sentences from radiological reports, but could not analyze more complicated sentences which appear frequently in medical reports. An important problem in medical NLP is, understanding how many codes or symbols are necessary to codify a medical domain completely. Another problem is determining whether existing medical lexicons like SNOMED-CT and ICD-9, etc. are suitable for representing the knowledge in medical reports unambiguously. This thesis investigates the problems behind current NLP systems and lexicons, and attempts to estimate the number of required symbols or codes to represent a large corpus of radiology reports. The knowledge will provide a greater understanding of how many symbols may be needed for the complete representation of concepts in other medical domains