12 research outputs found
Clinical coverage of an archetype repository over SNOMED-CT
AbstractClinical archetypes provide a means for health professionals to design what should be communicated as part of an Electronic Health Record (EHR). An ever-growing number of archetype definitions follow this health information modelling approach, and this international archetype resource will eventually cover a large number of clinical concepts. On the other hand, clinical terminology systems that can be referenced by archetypes also have a wide coverage over many types of health-care information.No existing work measures the clinical content coverage of archetypes using terminology systems as a metric. Archetype authors require guidance to identify under-covered clinical areas that may need to be the focus of further modelling effort according to this paradigm.This paper develops a first map of SNOMED-CT concepts covered by archetypes in a repository by creating a so-called terminological Shadow. This is achieved by mapping appropriate SNOMED-CT concepts from all nodes that contain archetype terms, finding the top two category levels of the mapped concepts in the SNOMED-CT hierarchy, and calculating the coverage of each category. A quantitative study of the results compares the coverage of different categories to identify relatively under-covered as well as well-covered areas. The results show that the coverage of the well-known National Health Service (NHS) Connecting for Health (CfH) archetype repository on all categories of SNOMED-CT is not equally balanced. Categories worth investigating emerged at different points on the coverage spectrum, including well-covered categories such as Attributes, Qualifier value, under-covered categories such as Microorganism, Kingdom animalia, and categories that are not covered at all such as Cardiovascular drug (product)
Combining ontologies and rules with clinical archetypes
Al igual que otros campos que dependen en gran medida de las funcionalidades ofrecidas por las tecnologías de la información y las comunicaciones (IT), la biomedicina y la salud necesitan cada vez más la implantación de normas y mecanismos ampliamente aceptados para el intercambio de datos, información y conocimiento. Dicha necesidad de compatibilidad e interoperabilidad va más allá de las cuestiones sintácticas y estructurales, pues la interoperabilidad semántica es también requerida. La interoperabilidad a nivel semántico es esencial para el soporte computarizado de alertas, flujos de trabajo y de la medicina basada en evidencia cuando contamos con la presencia de sistemas heterogéneos de Historia Clínica Electrónica (EHR). El modelo de arquetipos clínicos respaldado por el estándar CEN/ISO EN13606 y la fundación openEHR ofrece un mecanismo para expresar las estructuras de datos clínicos de manera compartida e interoperable. El modelo ha ido ganando aceptación en los últimos años por su capacidad para definir conceptos clínicos basados en un Modelo de Referencia común. Dicha separación a dos capas permite conservar la heterogeneidad de las implementaciones de almacenamiento a bajo nivel, presentes en los diferentes sistemas de EHR. Sin embargo, los lenguajes de arquetipos no soportan la representación de reglas clínicas ni el mapeo a ontologías formales, ambos elementos fundamentales para alcanzar la interoperabilidad semántica completa pues permiten llevar a cabo el razonamiento y la inferencia a partir del conocimiento clínico existente. Paralelamente, es reconocido el hecho de que la World Wide Web presenta requisitos análogos a los descritos anteriormente, lo cual ha fomentado el desarrollo de la Web Semántica. El progreso alcanzado en este terreno, con respecto a la representación del conocimiento y al razonamiento sobre el mismo, es combinado en esta tesis con los modelos de EHR con el objetivo de mejorar el enfoque de los arquetipos clínicos y ofrecer funcionalidades que se corresponden con nivel más alto de interoperabilidad semántica. Concretamente, la investigación que se describe a continuación presenta y evalúa un enfoque para traducir automáticamente las definiciones expresadas en el lenguaje de definición de arquetipos de openEHR (ADL) a una representación formal basada en lenguajes de ontologías. El método se implementa en la plataforma ArchOnt, que también es descrita. A continuación se estudia la integración de dichas representaciones formales con reglas clínicas, ofreciéndose un enfoque para reutilizar el razonamiento con instancias concretas de datos clínicos. Es importante ver como el acto de compartir el conocimiento clínico expresado a través de reglas es coherente con la filosofía de intercambio abierto fomentada por los arquetipos, a la vez que se extiende la reutilización a proposiciones de conocimiento declarativo como las utilizadas en las guías de práctica clínica. De esta manera, la tesis describe una técnica de mapeo de arquetipos a ontologías, para luego asociar reglas clínicas a la representación resultante. La traducción automática también permite la conexión formal de los elementos especificados en los arquetipos con conceptos clínicos equivalentes provenientes de otras fuentes como son las terminologías clínicas. Dichos enlaces fomentan la reutilización del conocimiento clínico ya representado, así como el razonamiento y la navegación a través de distintas ontologías clínicas. Otra contribución significativa de la tesis es la aplicación del enfoque mencionado en dos proyectos de investigación y desarrollo clínico, llevados a cabo en combinación con hospitales universitarios de Madrid. En la explicación se incluyen ejemplos de las aplicaciones más representativas del enfoque como es el caso del desarrollo de sistemas de alertas orientados a mejorar la seguridad del paciente. No obstante, la traducción automática de arquetipos clínicos a lenguajes de ontologías constituye una base común para la implementación de una amplia gama de actividades semánticas, razonamiento y validación, evitándose así la necesidad de aplicar distintos enfoques ad-hoc directamente sobre los arquetipos para poder satisfacer las condiciones de cada contexto
Combining ontologies and rules with clinical archetypes
Al igual que otros campos que dependen en gran medida de las funcionalidades ofrecidas por las tecnologías de la información y las comunicaciones (IT), la biomedicina y la salud necesitan cada vez más la implantación de normas y mecanismos ampliamente aceptados para el intercambio de datos, información y conocimiento. Dicha necesidad de compatibilidad e interoperabilidad va más allá de las cuestiones sintácticas y estructurales, pues la interoperabilidad semántica es también requerida. La interoperabilidad a nivel semántico es esencial para el soporte computarizado de alertas, flujos de trabajo y de la medicina basada en evidencia cuando contamos con la presencia de sistemas heterogéneos de Historia Clínica Electrónica (EHR). El modelo de arquetipos clínicos respaldado por el estándar CEN/ISO EN13606 y la fundación openEHR ofrece un mecanismo para expresar las estructuras de datos clínicos de manera compartida e interoperable. El modelo ha ido ganando aceptación en los últimos años por su capacidad para definir conceptos clínicos basados en un Modelo de Referencia común. Dicha separación a dos capas permite conservar la heterogeneidad de las implementaciones de almacenamiento a bajo nivel, presentes en los diferentes sistemas de EHR. Sin embargo, los lenguajes de arquetipos no soportan la representación de reglas clínicas ni el mapeo a ontologías formales, ambos elementos fundamentales para alcanzar la interoperabilidad semántica completa pues permiten llevar a cabo el razonamiento y la inferencia a partir del conocimiento clínico existente. Paralelamente, es reconocido el hecho de que la World Wide Web presenta requisitos análogos a los descritos anteriormente, lo cual ha fomentado el desarrollo de la Web Semántica. El progreso alcanzado en este terreno, con respecto a la representación del conocimiento y al razonamiento sobre el mismo, es combinado en esta tesis con los modelos de EHR con el objetivo de mejorar el enfoque de los arquetipos clínicos y ofrecer funcionalidades que se corresponden con nivel más alto de interoperabilidad semántica. Concretamente, la investigación que se describe a continuación presenta y evalúa un enfoque para traducir automáticamente las definiciones expresadas en el lenguaje de definición de arquetipos de openEHR (ADL) a una representación formal basada en lenguajes de ontologías. El método se implementa en la plataforma ArchOnt, que también es descrita. A continuación se estudia la integración de dichas representaciones formales con reglas clínicas, ofreciéndose un enfoque para reutilizar el razonamiento con instancias concretas de datos clínicos. Es importante ver como el acto de compartir el conocimiento clínico expresado a través de reglas es coherente con la filosofía de intercambio abierto fomentada por los arquetipos, a la vez que se extiende la reutilización a proposiciones de conocimiento declarativo como las utilizadas en las guías de práctica clínica. De esta manera, la tesis describe una técnica de mapeo de arquetipos a ontologías, para luego asociar reglas clínicas a la representación resultante. La traducción automática también permite la conexión formal de los elementos especificados en los arquetipos con conceptos clínicos equivalentes provenientes de otras fuentes como son las terminologías clínicas. Dichos enlaces fomentan la reutilización del conocimiento clínico ya representado, así como el razonamiento y la navegación a través de distintas ontologías clínicas. Otra contribución significativa de la tesis es la aplicación del enfoque mencionado en dos proyectos de investigación y desarrollo clínico, llevados a cabo en combinación con hospitales universitarios de Madrid. En la explicación se incluyen ejemplos de las aplicaciones más representativas del enfoque como es el caso del desarrollo de sistemas de alertas orientados a mejorar la seguridad del paciente. No obstante, la traducción automática de arquetipos clínicos a lenguajes de ontologías constituye una base común para la implementación de una amplia gama de actividades semánticas, razonamiento y validación, evitándose así la necesidad de aplicar distintos enfoques ad-hoc directamente sobre los arquetipos para poder satisfacer las condiciones de cada contexto
Clinical foundations and information architecture for the implementation of a federated health record service
Clinical care increasingly requires healthcare professionals to access patient record information that
may be distributed across multiple sites, held in a variety of paper and electronic formats, and
represented as mixtures of narrative, structured, coded and multi-media entries. A longitudinal
person-centred electronic health record (EHR) is a much-anticipated solution to this problem, but
its realisation is proving to be a long and complex journey.
This Thesis explores the history and evolution of clinical information systems, and establishes a set
of clinical and ethico-legal requirements for a generic EHR server. A federation approach (FHR) to
harmonising distributed heterogeneous electronic clinical databases is advocated as the basis for
meeting these requirements.
A set of information models and middleware services, needed to implement a Federated Health
Record server, are then described, thereby supporting access by clinical applications to a distributed
set of feeder systems holding patient record information. The overall information architecture thus
defined provides a generic means of combining such feeder system data to create a virtual
electronic health record. Active collaboration in a wide range of clinical contexts, across the whole
of Europe, has been central to the evolution of the approach taken.
A federated health record server based on this architecture has been implemented by the author
and colleagues and deployed in a live clinical environment in the Department of Cardiovascular
Medicine at the Whittington Hospital in North London. This implementation experience has fed
back into the conceptual development of the approach and has provided "proof-of-concept"
verification of its completeness and practical utility.
This research has benefited from collaboration with a wide range of healthcare sites, informatics
organisations and industry across Europe though several EU Health Telematics projects: GEHR,
Synapses, EHCR-SupA, SynEx, Medicate and 6WINIT.
The information models published here have been placed in the public domain and have
substantially contributed to two generations of CEN health informatics standards, including CEN
TC/251 ENV 13606
Uma arquitectura segura e colaborativa para registos de saúde electrónicos com suporte a mobilidade
Doutoramento em InformáticaDurante as ultimas décadas, os registos de saúde eletrónicos (EHR) têm
evoluído para se adaptar a novos requisitos. O cidadão tem-se envolvido
cada vez mais na prestação dos cuidados médicos, sendo mais pró ativo e
desejando potenciar a utilização do seu registo. A mobilidade do cidadão
trouxe mais desafios, a existência de dados dispersos, heterogeneidade de
sistemas e formatos e grande dificuldade de partilha e comunicação entre
os prestadores de serviços.
Para responder a estes requisitos, diversas soluções apareceram, maioritariamente
baseadas em acordos entre instituições, regiões e países. Estas abordagens
são usualmente assentes em cenários federativos muito complexos e
fora do controlo do paciente. Abordagens mais recentes, como os registos
pessoais de saúde (PHR), permitem o controlo do paciente, mas levantam
duvidas da integridade clinica da informação aos profissionais clínicos.
Neste cenário os dados saem de redes e sistemas controlados, aumentando
o risco de segurança da informação. Assim sendo, são necessárias novas
soluções que permitam uma colaboração confiável entre os diversos atores
e sistemas.
Esta tese apresenta uma solução que permite a colaboração aberta e segura
entre todos os atores envolvidos nos cuidados de saúde. Baseia-se numa
arquitetura orientada ao serviço, que lida com a informação clínica usando
o conceito de envelope fechado. Foi modelada recorrendo aos princípios
de funcionalidade e privilégios mínimos, com o propósito de fornecer proteção dos dados durante a transmissão, processamento e armazenamento.
O controlo de acesso _e estabelecido por políticas definidas pelo paciente.
Cartões de identificação eletrónicos, ou certificados similares são utilizados
para a autenticação, permitindo uma inscrição automática. Todos os
componentes requerem autenticação mútua e fazem uso de algoritmos de
cifragem para garantir a privacidade dos dados. Apresenta-se também um
modelo de ameaça para a arquitetura, por forma a analisar se as ameaças
possíveis foram mitigadas ou se são necessários mais refinamentos.
A solução proposta resolve o problema da mobilidade do paciente e a dispersão de dados, capacitando o cidadão a gerir e a colaborar na criação
e manutenção da sua informação de saúde. A arquitetura permite uma
colaboração aberta e segura, possibilitando que o paciente tenha registos
mais ricos, atualizados e permitindo o surgimento de novas formas de criar
e usar informação clínica ou complementar.Since their early adoption Electronic Health Records (EHR) have been evolving
to cope with increasing requirements from institutions, professionals
and, more recently, from patients. Citizens became more involved demanding
successively more control over their records and an active role on their
content. Mobility brought also new requirements, data become scattered
over heterogeneous systems and formats, with increasing di culties on data
sharing between distinct providers.
To cope with these challenges several solutions appeared, mostly based on
service level agreements between entities, regions and countries. They usually
required de ning complex federated scenarios and left the patient outside
the process. More recent approaches, such as personal health records
(PHR), enable patient control although raises clinical integrity doubts to
other actors, such as physicians. Also, information security risk increase as
data travels outside controlled networks and systems. To overcome this,
new solutions are needed to facilitate trustable collaboration between the
diverse actors and systems.
In this thesis we present a solution that enables a secure and open collaboration
between all healthcare actors. It is based on a service-oriented architecture
that deals with the clinical data using a closed envelope concept. The
architecture was modeled with minimal functionality and privileges bearing
in mind strong protection of data during transmission, processing and
storing. The access control is made through patient policies and authentication
uses electronic identi cation cards or similar certi cates, enabling
auto-enrollment. All the components require mutual authentication and
uses cyphering mechanisms to assure privacy. We also present a threat
model to verify, through our solution, if possible threats were mitigated or
if further re nement is needed.
The proposed solution solves the problem of patient mobility and data dispersion,
and empowers citizens to manage and collaborate in their personal
healthcare information. It also permits open and secure collaboration, enabling
the patient to have richer and up to date records that can foster new
ways to generate and use clinical or complementary information
Towards a system of concepts for Family Medicine. Multilingual indexing in General Practice/ Family Medicine in the era of Semantic Web
UNIVERSITY OF LIÈGE, BELGIUM
Executive Summary
Faculty of Medicine
Département Universitaire de Médecine Générale.
Unité de recherche Soins Primaires et Santé
Doctor in biomedical sciences
Towards a system of concepts for Family Medicine.
Multilingual indexing in General Practice/ Family Medicine in the era
of SemanticWeb
by Dr. Marc JAMOULLE
Introduction
This thesis is about giving visibility to the often overlooked work of family
physicians and consequently, is about grey literature in General Practice
and Family Medicine (GP/FM). It often seems that conference organizers
do not think of GP/FM as a knowledge-producing discipline that deserves
active dissemination. A conference is organized, but not much is done with
the knowledge shared at these meetings. In turn, the knowledge cannot be
reused or reapplied. This these is also about indexing. To find knowledge
back, indexing is mandatory. We must prepare tools that will automatically
index the thousands of abstracts that family doctors produce each year in
various languages. And finally this work is about semantics1. It is an introduction
to health terminologies, ontologies, semantic data, and linked
open data. All are expressions of the next step: Semantic Web for health
care data. Concepts, units of thought expressed by terms, will be our target
and must have the ability to be expressed in multiple languages. In turn,
three areas of knowledge are at stake in this study: (i) Family Medicine as a
pillar of primary health care, (ii) computational linguistics, and (iii) health
information systems.
Aim
• To identify knowledge produced by General practitioners (GPs) by
improving annotation of grey literature in Primary Health Care
• To propose an experimental indexing system, acting as draft for a
standardized table of content of GP/GM
• To improve the searchability of repositories for grey literature in GP/GM.
1For specific terms, see the Glossary page 257
x
Methods
The first step aimed to design the taxonomy by identifying relevant concepts
in a compiled corpus of GP/FM texts. We have studied the concepts
identified in nearly two thousand communications of GPs during
conferences. The relevant concepts belong to the fields that are focusing
on GP/FM activities (e.g. teaching, ethics, management or environmental
hazard issues).
The second step was the development of an on-line, multilingual, terminological
resource for each category of the resulting taxonomy, named
Q-Codes. We have designed this terminology in the form of a lightweight
ontology, accessible on-line for readers and ready for use by computers of
the semantic web. It is also fit for the Linked Open Data universe.
Results
We propose 182 Q-Codes in an on-line multilingual database (10 languages)
(www.hetop.eu/Q) acting each as a filter for Medline. Q-Codes are also available
under the form of Unique Resource Identifiers (URIs) and are exportable
in Web Ontology Language (OWL). The International Classification of Primary
Care (ICPC) is linked to Q-Codes in order to form the Core Content
Classification in General Practice/Family Medicine (3CGP). So far, 3CGP is
in use by humans in pedagogy, in bibliographic studies, in indexing congresses,
master theses and other forms of grey literature in GP/FM. Use by
computers is experimented in automatic classifiers, annotators and natural
language processing.
Discussion
To the best of our knowledge, this is the first attempt to expand the ICPC
coding system with an extension for family physician contextual issues,
thus covering non-clinical content of practice. It remains to be proven that
our proposed terminology will help in dealing with more complex systems,
such as MeSH, to support information storage and retrieval activities.
However, this exercise is proposed as a first step in the creation of an ontology
of GP/FM and as an opening to the complex world of Semantic Web
technologies.
Conclusion
We expect that the creation of this terminological resource for indexing abstracts
and for facilitating Medline searches for general practitioners, researchers
and students in medicine will reduce loss of knowledge in the
domain of GP/FM. In addition, through better indexing of the grey literature
(congress abstracts, master’s and doctoral theses), we hope to enhance
the accessibility of research results and give visibility to the invisible work
of family physicians
Conceptualization of Computational Modeling Approaches and Interpretation of the Role of Neuroimaging Indices in Pathomechanisms for Pre-Clinical Detection of Alzheimer Disease
With swift advancements in next-generation sequencing technologies alongside the voluminous growth of biological data, a diversity of various data resources such as databases and web services have been created to facilitate data management, accessibility, and analysis. However, the burden of interoperability between dynamically growing data resources is an increasingly rate-limiting step in biomedicine, specifically concerning neurodegeneration. Over the years, massive investments and technological advancements for dementia research have resulted in large proportions of unmined data. Accordingly, there is an essential need for intelligent as well as integrative approaches to mine available data and substantiate novel research outcomes. Semantic frameworks provide a unique possibility to integrate multiple heterogeneous, high-resolution data resources with semantic integrity using standardized ontologies and vocabularies for context- specific domains. In this current work, (i) the functionality of a semantically structured terminology for mining pathway relevant knowledge from the literature, called Pathway Terminology System, is demonstrated and (ii) a context-specific high granularity semantic framework for neurodegenerative diseases, known as NeuroRDF, is presented. Neurodegenerative disorders are especially complex as they are characterized by widespread manifestations and the potential for dramatic alterations in disease progression over time. Early detection and prediction strategies through clinical pointers can provide promising solutions for effective treatment of AD. In the current work, we have presented the importance of bridging the gap between clinical and molecular biomarkers to effectively contribute to dementia research. Moreover, we address the need for a formalized framework called NIFT to automatically mine relevant clinical knowledge from the literature for substantiating high-resolution cause-and-effect models