Dispositions and the Infectious Disease Ontology

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations

Ontological representation of CDC Active Bacterial Core Surveillance Case Reports

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes

Exploring system behavior in a system ontology

Understanding and modeling system behavior is a key aspect of many disciplines, and is crucial when systems are designed to manifest desirable behaviors. In order to grasp system behavior, it is inevitable to address how it emerges from the properties and behaviors of interrelated system components. In pursuit of an understanding of the emergence phenomenon and to account for the nature of emergent system behavior, this paper takes a first step in extending a system core ontology with behavioral aspects. The ontology extension is grounded on the Unified Foundational Ontology and also in system science definitions and disposition theories.</p

OBML - Ontologies in Biomedicine and Life Sciences

The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2(nd) in a series of meetings organized by the Working Group “Ontologies in Biomedicine and Life Sciences” of the German Society of Computer Science (GI) and the German Society of Medical Informatics, Biometry and Epidemiology (GMDS). Integrating, processing and applying the rapidly expanding information generated in the life sciences — from public health to clinical care and molecular biology — is one of the most challenging problems that research in these fields is facing today. As the amounts of experimental data, clinical information and scientific knowledge increase, there is a growing need to promote interoperability of these resources, support formal analyses, and to pre-process knowledge for further use in problem solving and hypothesis formulation. The OBML workshop series pursues the aim of gathering scientists who research topics related to life science ontologies, to exchange ideas, discuss new results and establish relationships. The OBML group promotes the collaboration between ontologists, computer scientists, bio-informaticians and applied logicians, as well as the cooperation with physicians, biologists, biochemists and biometricians, and supports the establishment of this new discipline in research and teaching. Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies to science and medicine. A total of 14 papers were presented, and from these we selected four manuscripts for inclusion in this special issue. An interdisciplinary audience from all areas related to biomedical ontologies attended OBML 2010. In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences. The next event emphasizes the special topic of the ontology of phenotypes, in Berlin, Germany on October 6-7, 2011

Representing dispositions

Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will discuss some of the results of the philosophical debate about dispositions, in order to see whether the formal relations needed to represent dispositions can be broken down to binary relations. Finally, we will discuss problems arising from the possibility of the absence of realizations, of multi-track or multi-trigger dispositions and offer suggestions on how to deal with them

A System Core Ontology for Capability Emergence Modeling

To properly understand organizational adaptation and innovation, it is critical to understand the emergence phenomenon, i.e., how the capabilities of a system emerge after changes. However, for this, we should be able to explain systems, their structure, behavior, and capabilities. In pursuit of an understanding of the emergence phenomenon and the nature of those new kinds of systems in organizations, we propose a well-founded system core ontology based on the Unified Foundational Ontology. The ontology is also grounded in system science definitions and disposition theories. For a more integrated explanation of emergence, the proposed ontology considers distinct perspectives of a system, such as its composition, structure, properties, and functions. In the end, we discuss the applications and implications of the proposed ontology on the enterprise architecture area and emergence modeling

The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

UMA ONTOLOGIA DE AGRAVOS CAUSADOS PELO USO INADEQUADO DE AGROTÓXICOS

The indiscriminate use of pesticides is one of the main factors contributing towards the chemical contamination of human beings, causing various types of intoxications. However, accessing information about pesticides and the consequences of their use, has proven difficult. Therefore, the present paper describes the development of an ontology which has the purpose of structuring knowledge in the field of health, focusing on diseases caused by the improper and indiscriminate use of pesticides. The ontology developed, called OntoTox was based on documents with a pesticide classification and the intoxication caused by their use.  OntoTox was constructed according to the Methontology method, as well as some steps of the 101 method and implemented in the Protégé environment. This ontology was evaluated by the Data-Driven method as well as the response to questionnaires administered to experts in the fields of health and agriculture. They considered it a valid source of knowledge in aiding the diagnosis of poisoning and health problems related to the use of pesticides. This ontology can be used in providing aid to victims of poisoning and in research involving pesticides and poisoning.O uso indiscriminado de agrotóxicos é um dos principais fatores que contribuem para a contaminação química dos seres humanos, causando vários tipos de intoxicações. No entanto, o acesso a informações sobre os pesticidas e as consequências de seu uso tem sido difícil. Portanto, o presente artigo descreve o desenvolvimento de uma ontologia que tem a finalidade de estruturar conhecimentos no campo da saúde, incidindo sobre doenças causadas pelo uso indevido e indiscriminado de pesticidas. A ontologia desenvolvida, chamada OntoTox, foi baseada em documentos com classificação de pesticidas e da intoxicação causada pelo seu uso. OntoTox foi construída de acordo com o método Methontology, bem como algumas fases do método 101 e implementada no ambiente Protégé. Esta ontologia foi avaliada pelo método orientado a dados, bem como a resposta a questionários aplicados com especialistas nas áreas de saúde e agricultura. Eles a consideraram uma fonte válida de conhecimento para ajudar no diagnóstico de problemas de intoxicação e de saúde relacionados ao uso de pesticidas. Esta ontologia pode ser utilizada na prestação de ajuda às vítimas de envenenamento e na pesquisa com agrotóxicos e intoxicação