Supporting Special-Purpose Health Care Models via Web Interfaces

The potential of the Web, via both the Internet and intranets, to facilitate development of clinical information systems has been evident for some time. Most Web-based clinical workstations interfaces, however, provide merely a loose collection of access channels. There are numerous examples of systems for access to either patient data or clinical guidelines, but only isolated cases where clinical decision support is presented integrally with the process of patient care, in particular, in the form of active alerts and reminders based on patient data. Moreover, pressures in the health industry are increasing the need for doctors to practice in accordance with ¿best practice¿ guidelines and often to operate under novel health-care arrangements. We present the Care Plan On-Line (CPOL) system, which provides intranet-based support for the SA HealthPlus Coordinated Care model for chronic disease management. We describe the interface design rationale of CPOL and its implementation framework, which is flexible and broadly applicable to support new health care models over intranets or the Internet

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the proposed workflow we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip Human Exon 1.0 ST Array

PRODUCT LINE ARCHITECTURE FOR HADRONTHERAPY CONTROL SYSTEM: APPLICATIONS DEVELOPMENT AND CERTIFICATION

Hadrontherapy is the treatment of cancer with charged ion beams. As the charged ion beams used in hadrontherapy are required to be accelerated to very large energies, the particle accelerators used in this treatment are complex and composed of several sub-systems. As a result, control systems are employed for the supervision and control of these accelerators. Currently, The Italian National Hadrontherapy Facility (CNAO) has the objective of modernizing one of the software environments of its control system. Such a project would allow for the integration of new types of devices into the control system, such as mobile devices, as well as introducing newer technologies into the environment. In order to achieve this, this work began with the requirement analysis and definition of a product line architecture for applications of the upgraded control system environment. The product line architecture focuses on reliability, maintainability, and ease of compliance with medical software certification directives. This was followed by the design and development of several software services aimed at allowing the communication of the environments applications and other components of the control system, such as remote file access, relational data access, and OPC-UA. In addition, several libraries and tools have been developed to support the development of future control system applications, following the defined product line architecture. Lastly, a pilot application was created using the tools developed during this work, as well as the preliminary results of a cross-environment integration project. The approach followed in this work is later evaluated by comparing the developed tools to their legacy counterparts, as well as estimating the impact of future applications following the defined product line architecture.Hadrontherapy is the treatment of cancer with charged ion beams. As the charged ion beams used in hadrontherapy are required to be accelerated to very large energies, the particle accelerators used in this treatment are complex and composed of several sub-systems. As a result, control systems are employed for the supervision and control of these accelerators. Currently, The Italian National Hadrontherapy Facility (CNAO) has the objective of modernizing one of the software environments of its control system. Such a project would allow for the integration of new types of devices into the control system, such as mobile devices, as well as introducing newer technologies into the environment. In order to achieve this, this work began with the requirement analysis and definition of a product line architecture for applications of the upgraded control system environment. The product line architecture focuses on reliability, maintainability, and ease of compliance with medical software certification directives. This was followed by the design and development of several software services aimed at allowing the communication of the environments applications and other components of the control system, such as remote file access, relational data access, and OPC-UA. In addition, several libraries and tools have been developed to support the development of future control system applications, following the defined product line architecture. Lastly, a pilot application was created using the tools developed during this work, as well as the preliminary results of a cross-environment integration project. The approach followed in this work is later evaluated by comparing the developed tools to their legacy counterparts, as well as estimating the impact of future applications following the defined product line architecture

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM , which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

<p>Abstract</p> <p>Background</p> <p>To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory.</p> <p>Results</p> <p>To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data.</p> <p>Conclusions</p> <p>We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.</p

A Community-Driven Validation Service for Standard Medical Imaging Objects

Digital medical imaging laboratories contain many distinct types of equipment provided by different manufacturers. Interoperability is a critical issue and the DICOM protocol is a de facto standard in those environments. However, manufacturers' implementation of the standard may have non-conformities at several levels, which will hinder systems' integration. Moreover, medical staff may be responsible for data inconsistencies when entering data. Those situations severely affect the quality of healthcare services since they can disrupt system operations. The existence of software able to confirm data quality and compliance with the DICOM standard is important for programmers, IT staff and healthcare technicians. Although there are a few solutions that try to accomplish this goal, they are unable to deal with certain situations that require user input. Furthermore, these cases usually require the setup of a working environment, which makes the sharing of validation information more difficult. This article proposes and describes the development of a Web DICOM validation service for the community. This solution requires no configuration by the user, promotes validation results share-ability in the community and preserves patient data privacy since files are de-identified on the client side.Comment: Computer Standards & Interfaces, 201

Workshop on the EHCR

This deliverable provides a summary report of a workshop on Electronic Health Records that was organised and delivered as the main focus of Workpackage 16 of the Semantic Mining project. The workshop was held as day three of a three-day series of events held in Brussels in late November 2004, under the umbrella and with kind support of the EUROREC organisation. This report provides a brief summary of that event, and includes in Annex 1 the complete delegate pack as printed and issued to all persons attending the event, This delegate pack included printed copies of all slides and screenshots used throughout the day. The workshop was well attended, and in particular the organisers are pleased to report that some very productive discussions took place that will act as the stimulus for new threads of research collaboration between various Semantic Mining partners, under the work plan of Workpackage 26. The organisers are grateful for the support of the EUROREC organisation in facilitating the organisation of this workshop and for lending their support to it through their web site and a personal endorsement of the event

The role of metaphor in user interface design

The thesis discusses the question of how unfamiliar computing systems, particularly those with graphical user interfaces, are learned and used. In particular, the approach of basing the design and behaviour of on-screen objects in the system's model world on a coherent theme and employing a metaphor is explored. The drawbacks, as well as the advantages, of this approach are reviewed and presented. The use of metaphors is also contrasted with other forms of users' mental models of interactive systems, and the need to provide a system image from which useful mental models can be developed is presented. Metaphors are placed in the context of users' understanding of interactive systems and novel application is made of the Qualitative Process Theory (QPT) qualitative reasoning model to reason about the behaviour of on-screen objects, the underlying system functionality, and the relationship between the two. This analysis supports reevaluation of the domains between which user interface metaphors are said to form mappings. A novel user interface design, entitled Medusa, that adopts guidelines for the design of metaphor-based systems, and for helping the user develop successful mental models, based on the QPT analysis and an empirical study of a popular metaphor-based system, is described. The first Medusa design is critiqued using well-founded usability inspection method. Employing the Lakoff/Johnson theory, a revised version of the Medusa user interface is described that derives its application semantics and dialogue structures from the entailments of the knowledge structures that ground understanding of the interface metaphor and that capture notions of embodiment in interaction with computing devices that QPT descriptions cannot. Design guidelines from influential existing work, and new methods of reasoning about metaphor-based designs, are presented with a number of novel graphical user interface designs intended to overcome the failings of existing systems and design approaches