52 research outputs found
Automatically Restructuring Practice Guidelines using the GEM DTD
This paper describes a system capable of semi-automatically filling an XML
template from free texts in the clinical domain (practice guidelines). The XML
template includes semantic information not explicitly encoded in the text
(pairs of conditions and actions/recommendations). Therefore, there is a need
to compute the exact scope of conditions over text sequences expressing the
required actions. We present a system developed for this task. We show that it
yields good performance when applied to the analysis of French practice
guidelines
From Texts to Structured Documents: The Case of Health Practice Guidelines
This paper describes a system capable of semi-automatically filling an XML
template from free texts in the clinical domain (practice guidelines). The XML
template includes semantic information not explicitly encoded in the text
(pairs of conditions and actions/recommendations). Therefore, there is a need
to compute the exact scope of conditions over text sequences expressing the
required actions. We present in this paper the rules developed for this task.
We show that the system yields good performance when applied to the analysis of
French practice guidelines
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Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems
There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings
Internet based molecular collaborative and publishing tools
The scientific electronic publishing model has hitherto been an Internet based delivery of electronic articles that are essentially replicas of their paper counterparts. They contain little in the way of added semantics that may better expose the science, assist the peer review process and facilitate follow on collaborations, even though the enabling technologies have been around for some time and are mature. This thesis will examine the evolution of chemical electronic publishing over the past 15 years. It will illustrate, which the help of two frameworks, how publishers should be exploiting technologies to improve the semantics of chemical journal articles, namely their value added features and relationships with other chemical resources on the Web.
The first framework is an early exemplar of structured and scalable electronic publishing where a Web content management system and a molecular database are integrated. It employs a test bed of articles from several RSC journals and supporting molecular coordinate and connectivity information. The value of converting 3D molecular expressions in chemical file formats, such as the MOL file, into more generic 3D graphics formats, such as Web3D, is assessed. This exemplar highlights the use of metadata management for bidirectional hyperlink maintenance in electronic publishing.
The second framework repurposes this metadata management concept into a Semantic Web application called SemanticEye. SemanticEye demonstrates how relationships between chemical electronic articles and other chemical resources are established. It adapts the successful semantic model used for digital music metadata management by popular applications such as iTunes. Globally unique identifiers enable relationships to be established between articles and other resources on the Web and SemanticEye implements two: the Document Object Identifier (DOI) for articles and the IUPAC International Chemical Identifier (InChI) for molecules. SemanticEye’s potential as a framework for seeding collaborations between researchers, who have hitherto never met, is explored using FOAF, the friend-of-a-friend Semantic Web standard for social networks
Metadata for user-centred, inclusive access to digital resources: realising the theory of AccessForAll Accessibility
To be inclusive, the Web needs published resources to be matched to individual users’ needs and preferences for their perception and control. In a decade, this has not been achieved and many cannot make use of resources despite having appropriate facilities. This thesis argues that the necessary management of resources can be achieved with well-designed metadata. Demonstration and explanation of the accessibility problems, efforts to solve them and the current state of inaccessibility of Web resources, any resource that is available through the World Wide Web, is fundamental to the research. The author relies heavily on Dublin Core metadata as it is relatively easy to use; is probably the most populous metadata; can be managed with free software systems, and for commercial reasons. The research investigated what makes DC metadata, so apparently simple, powerful enough to be the most popular metadata because there is very little available that explains this. The thesis then documents the scientific view of metadata upon which effective use of metadata can be based in the context of accessibility. It argues, at a practical level, that metadata is essential and integral to any shift to an on-going process approach to accessibility. It contributes to the science of metadata in as much as it analyses, synthesizes, and articulates the characteristics of an essential infrastructure for a new approach to accessibility. The author argues in favour of an on-going process approach to accessibility of resources that supports continuous improvement of any given resource, not necessarily by the author of the resource, and not necessarily by design or with knowledge of the original author, by contributors who may be distributed globally. The thesis argues that the current dependence on production guidelines and post-production evaluation of resources as either universally accessible or otherwise, does not adequately provide for either the accessibility necessary for individuals or the continuous or evolutionary approach possible within the current Web environment. It argues that a distributed, social-networking view of the Web as interactive, combined with a social model of disability, given the management tools of machine-readable, interoperable AccessForAll metadata, as developed, can achieve the desired goals. It raises issues regarding its implementation in the distributed environment of the Web
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A modular, open-source information extraction framework for identifying clinical concepts and processes of care in clinical narratives
In this thesis, a synthesis is presented of the knowledge models required by clinical informa- tion systems that provide decision support for longitudinal processes of care. Qualitative research techniques and thematic analysis are novelly applied to a systematic review of the literature on the challenges in implementing such systems, leading to the development of an original conceptual framework. The thesis demonstrates how these process-oriented systems make use of a knowledge base derived from workflow models and clinical guidelines, and argues that one of the major barriers to implementation is the need to extract explicit and implicit information from diverse resources in order to construct the knowledge base. Moreover, concepts in both the knowledge base and in the electronic health record (EHR) must be mapped to a common ontological model. However, the majority of clinical guideline information remains in text form, and much of the useful clinical information residing in the EHR resides in the free text fields of progress notes and laboratory reports. In this thesis, it is shown how natural language processing and information extraction techniques provide a means to identify and formalise the knowledge components required by the knowledge base. Original contributions are made in the development of lexico-syntactic patterns and the use of external domain knowledge resources to tackle a variety of information extraction tasks in the clinical domain, such as recognition of clinical concepts, events, temporal relations, term disambiguation and abbreviation expansion. Methods are developed for adapting existing tools and resources in the biomedical domain to the processing of clinical texts, and approaches to improving the scalability of these tools are proposed and evalu- ated. These tools and techniques are then combined in the creation of a novel approach to identifying processes of care in the clinical narrative. It is demonstrated that resolution of coreferential and anaphoric relations as narratively and temporally ordered chains provides a means to extract linked narrative events and processes of care from clinical notes. Coreference performance in discharge summaries and progress notes is largely dependent on correct identification of protagonist chains (patient, clinician, family relation), pronominal resolution, and string matching that takes account of experiencer, temporal, spatial, and anatomical context; whereas for laboratory reports additional, external domain knowledge is required. The types of external knowledge and their effects on system performance are identified and evaluated. Results are compared against existing systems for solving these tasks and are found to improve on them, or to approach the performance of recently reported, state-of-the- art systems. Software artefacts developed in this research have been made available as open-source components within the General Architecture for Text Engineering framework
Personal Knowledge Models with Semantic Technologies
Conceptual Data Structures (CDS) is a unified meta-model for representing knowledge cues in varying degrees of granularity, structuredness, and formality.
CDS consists of: (1) A simple, expressive data-model; (2) A relation ontology which unifies the relations found in cognitive models of personal knowledge management tools, e. g., documents, mind-maps, hypertext, or semantic wikis. (3) An interchange format for structured text. Implemented prototypes have been evaluated
Classification management and use in a networked environment : the case of the Universal Decimal Classification
In the Internet information space, advanced information retrieval (IR) methods and automatic text processing are used in conjunction with traditional knowledge organization systems (KOS). New information technology provides a platform for better KOS publishing, exploitation and sharing both for human and machine use. Networked KOS services are now being planned and developed as powerful tools for resource discovery. They will enable automatic contextualisation, interpretation and query matching to different indexing languages. The Semantic Web promises to be an environment in which the quality of semantic relationships in bibliographic classification systems can be fully exploited. Their use in the networked environment is, however, limited by the fact that they are not prepared or made available for advanced machine processing. The UDC was chosen for this research because of its widespread use and its long-term presence in online information retrieval systems. It was also the first system to be used for the automatic classification of Internet resources, and the first to be made available as a classification tool on the Web. The objective of this research is to establish the advantages of using UDC for information retrieval in a networked environment, to highlight the problems of automation and classification exchange, and to offer possible solutions. The first research question was is there enough evidence of the use of classification on the Internet to justify further development with this particular environment in mind? The second question is what are the automation requirements for the full exploitation of UDC and its exchange? The third question is which areas are in need of improvement and what specific recommendations can be made for implementing the UDC in a networked environment? A summary of changes required in the management and development of the UDC to facilitate its full adaptation for future use is drawn from this analysis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo
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