Heart failure ontology

Abstract Ontology represents explicit specification of knowledge in a specific domain of interest in the form of concepts and relations among them. This paper presents a medical ontology describing the domain of heart failure (HF). Construction of ontology for a domain like HF is recognized as an important step in systematization of existing medical knowledge. The main virtue of ontology is that the represented knowledge is both computer and humanreadable. The current development of the HF ontology is one of the main results of the EU Heartfaid project. The ontology has been implemented using Ontology Web Language and Protégé editing tool. It consists of roughly 200 classes, 100 relations and 2000 instances. The ontology is a precise, voluminous, portable, and upgradable representation of the HF domain. It is also a useful framework for building knowledge based systems in the HF domain, as well as for unambiguous communication between professionals. In the process of developing the HF ontology there have been significant technical and medical dilemmas. The current result should not be treated as the ultimate solution but as a starting point that will stimulate further research and development activities that can be very relevant for both intelligent computer systems and precise communication of medical knowledge

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

In cellular physiology and signaling, reactive oxygen species (ROS) play one of the most critical roles. ROS overproduction leads to cellular oxidative stress. This may lead to an irrecoverable imbalance of redox (oxidation-reduction reaction) function that deregulates redox homeostasis, which itself could lead to several diseases including neurodegenerative disease, cardiovascular disease, and cancers. In this study, we focus on the redox effects related to vascular systems in mammals. To support research in this domain, we developed an online knowledge base, DES-RedoxVasc, which enables exploration of information contained in the biomedical scientific literature. The DES-RedoxVasc system analyzed 233399 documents consisting of PubMed abstracts and PubMed Central full-text articles related to different aspects of redox biology in vascular systems. It allows researchers to explore enriched concepts from 28 curated thematic dictionaries, as well as literature-derived potential associations of pairs of such enriched concepts, where associations themselves are statistically enriched. For example, the system allows exploration of associations of pathways, diseases, mutations, genes/proteins, miRNAs, long ncRNAs, toxins, drugs, biological processes, molecular functions, etc. that allow for insights about different aspects of redox effects and control of processes related to the vascular system. Moreover, we deliver case studies about some existing or possibly novel knowledge regarding redox of vascular biology demonstrating the usefulness of DES-RedoxVasc. DES-RedoxVasc is the first compiled knowledge base using text mining for the exploration of this topic

LinkedScales : bases de dados em multiescala

Orientador: André SantanchèTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: As ciências biológicas e médicas precisam cada vez mais de abordagens unificadas para a análise de dados, permitindo a exploração da rede de relacionamentos e interações entre elementos. No entanto, dados essenciais estão frequentemente espalhados por um conjunto cada vez maior de fontes com múltiplos níveis de heterogeneidade entre si, tornando a integração cada vez mais complexa. Abordagens de integração existentes geralmente adotam estratégias especializadas e custosas, exigindo a produção de soluções monolíticas para lidar com formatos e esquemas específicos. Para resolver questões de complexidade, essas abordagens adotam soluções pontuais que combinam ferramentas e algoritmos, exigindo adaptações manuais. Abordagens não sistemáticas dificultam a reutilização de tarefas comuns e resultados intermediários, mesmo que esses possam ser úteis em análises futuras. Além disso, é difícil o rastreamento de transformações e demais informações de proveniência, que costumam ser negligenciadas. Este trabalho propõe LinkedScales, um dataspace baseado em múltiplos níveis, projetado para suportar a construção progressiva de visões unificadas de fontes heterogêneas. LinkedScales sistematiza as múltiplas etapas de integração em escalas, partindo de representações brutas (escalas mais baixas), indo gradualmente para estruturas semelhantes a ontologias (escalas mais altas). LinkedScales define um modelo de dados e um processo de integração sistemático e sob demanda, através de transformações em um banco de dados de grafos. Resultados intermediários são encapsulados em escalas reutilizáveis e transformações entre escalas são rastreadas em um grafo de proveniência ortogonal, que conecta objetos entre escalas. Posteriormente, consultas ao dataspace podem considerar objetos nas escalas e o grafo de proveniência ortogonal. Aplicações práticas de LinkedScales são tratadas através de dois estudos de caso, um no domínio da biologia -- abordando um cenário de análise centrada em organismos -- e outro no domínio médico -- com foco em dados de medicina baseada em evidênciasAbstract: Biological and medical sciences increasingly need a unified, network-driven approach for exploring relationships and interactions among data elements. Nevertheless, essential data is frequently scattered across sources with multiple levels of heterogeneity. Existing data integration approaches usually adopt specialized, heavyweight strategies, requiring a costly upfront effort to produce monolithic solutions for handling specific formats and schemas. Furthermore, such ad-hoc strategies hamper the reuse of intermediary integration tasks and outcomes. This work proposes LinkedScales, a multiscale-based dataspace designed to support the progressive construction of a unified view of heterogeneous sources. It departs from raw representations (lower scales) and goes towards ontology-like structures (higher scales). LinkedScales defines a data model and a systematic, gradual integration process via operations over a graph database. Intermediary outcomes are encapsulated as reusable scales, tracking the provenance of inter-scale operations. Later, queries can combine both scale data and orthogonal provenance information. Practical applications of LinkedScales are discussed through two case studies on the biology domain -- addressing an organism-centric analysis scenario -- and the medical domain -- focusing on evidence-based medicine dataDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação141353/2015-5CAPESCNP

An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

Ontology-driven monitoring of patient's vital signs enabling personalized medical detection and alert

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Ontologie e modellazione di dati sanitari - Attivit? di ricerca nell\u27ambito del progetto ODINET

The Odinet project has as its primary objective to conduct research and development aimed at defining a technological framework for online access and dissemination of structured and heterogeneous data. This report carried out a survey of the main methods of modeling for the identification, cataloging and presentation of data on the Web. In particular, the purpose is to provide guidance on what specific technologies to be adopted in the field of Semantic Web and Linked Open Data, in order to be able to exploit the best information contained in the Public Administration data regarding the healthcare domain

Ontology for Psychophysiological Dysregulation of Anger/Aggression

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge. In this project, we developed a software program that assists clinicians in making diagnostic decisions about a particular problem type called ‘psychophysiological dysregulation of anger/aggression’. We created a new ontology for the problem domain. The computer program asks a set of pertinent questions and the patient or clinician on behalf of the patient is required to answer it. All these answers along with the results from various lab assessment tests are fed into the software program which then outputs a diagnosis by interacting with the ontology and also proposes the preferred treatment plan. While undergoing the treatment the patient is monitored at regular intervals by the clinician and this data is recorded as the treatment episode data. The tools and technologies used for this project are Web Ontology Language (OWL) version 2, Protégé 4.1.0 Beta, Java, Eclipse Helios IDE and IBM DB2. Adviser: Jitender S. Deogu

Redox control of vascular biology

Redox control is lost when the antioxidant defense system cannot remove abnormally high concentrations of signaling molecules, such as reactive oxygen species (ROS). Chronically elevated levels of ROS cause oxidative stress that may eventually lead to cancer and cardiovascular and neurodegenerative diseases. In this review, we focus on redox effects in the vascular system. We pay close attention to the subcompartments of the vascular system (endothelium, smooth muscle cell layer) and give an overview of how redox changes influence those different compartments. We also review the core aspects of redox biology, cardiovascular physiology, and pathophysiology. Moreover, the topic-specific knowledgebase DES-RedoxVasc was used to develop two case studies, one focused on endothelial cells and the other on the vascular smooth muscle cells, as a starting point to possibly extend our knowledge of redox control in vascular biology. © 2019 The Authors. BioFactors published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology

Ontology for Psychophysiological Dysregulation of Anger/Aggression

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge. In this project, we developed a software program that assists clinicians in making diagnostic decisions about a particular problem type called ‘psychophysiological dysregulation of anger/aggression’. We created a new ontology for the problem domain. The computer program asks a set of pertinent questions and the patient or clinician on behalf of the patient is required to answer it. All these answers along with the results from various lab assessment tests are fed into the software program which then outputs a diagnosis by interacting with the ontology and also proposes the preferred treatment plan. While undergoing the treatment the patient is monitored at regular intervals by the clinician and this data is recorded as the treatment episode data. The tools and technologies used for this project are Web Ontology Language (OWL) version 2, Protégé 4.1.0 Beta, Java, Eclipse Helios IDE and IBM DB2. Adviser: Jitender S. Deogu