The Epilepsy Ontology: a community-based ontology tailored for semantic interoperability and text-mining

Motivation: Epilepsy is a multi-faceted complex disorder that requires a precise understanding of the classification, diagnosis, treatment, and disease mechanism governing it. Although scattered resources are available on epilepsy, comprehensive and structured knowledge is missing. In contemplation to promote multidisciplinary knowledge exchange and facilitate advancement in clinical management, especially in pre-clinical research, a disease-specific ontology is necessary. The presented ontology is designed to enable better interconnection between scientific community members in the epilepsy domain.Results: The Epilepsy Ontology (EPIO) is an assembly of structured knowledge on various aspects of epilepsy, developed according to Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) Foundry principles. Concepts and definitions are collected from the latest International League against Epilepsy (ILAE) classification, domain-specific ontologies, and scientific literature. This ontology consists of 1,879 classes and 28,151 axioms (2,171 declaration axioms, 2,219 logical axioms) from several aspects of epilepsy. This ontology is intended to be used for data management and text mining purposes.

Towards a Unified Dispositional Framework for Realizable Entities

Realizable entities are properties that can be realized in processes of specific correlated types in which the bearer participates. It will be valuable to create a systematic classification of realizable entities because they are useful for various modeling purposes in ontologies. In this paper we outline a unifying framework for realizable entities (including dispositions and roles) in the upper ontology Basic Formal Ontology (BFO) that is theoretically underpinned by J. McKitrick’s pragmatic approach to dispositions. In particular, we develop a formal ontological account of “extrinsic dispositions” and illustrate its potential applications with clarification of functions and roles in BFO.

Approaching Healthy City Ontology: First-Level Classes Definition Using BFO

In recent decades, the concept of the healthy city (HC) has become more and more relevant in many fields, such as city administration and scientific environment, and has become a commonly understood concept in the general public. Due to the breakneck growth of people living in urban contexts, the subsequent necessity to guarantee good urban conditions for all kinds of citizens, and the general deterioration of the hearth environment caused by human activities (concentrated in urban settlements), this issue is increasing in its relevance. In this paper, the authors discuss the concept of the HC from an ontological point of view to organize the highly complex system of elements and the mutual relations that constitute the idea of HC. The main goals of an HC are quite intuitive, but the number of components that define and manage it is vast and related to different disciplines: sustainability, urban management, urban planning, and health and social studies. With the presented research, the authors intend to start an organizational definition of the HC using basic formal ontology (BFO). Considering the definition of HC, the authors focus on the ontology process and the different typologies of ontological structures. Then, the authors describe a first-level scheme of HC ontology and, finally, discuss possible applications of the presented study and next research steps.

BFO-based ontology enhancement to promote interoperability in BIM

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information.

An Ontological Approach to Enhancing Information Sharing in Disaster Response

Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders (ERs) may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary resolves inconsistent terminologies and promotes semantic interoperability among ERs. In this work, we discuss developing POLARISCO as an extension of Basic Formal Ontology (BFO) and the Common Core Ontologies (CCO). We conclude by presenting a real use-case to check the efficiency and applicability of the proposed ontology.

TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties

Traditional Chinese drugs (TCDs) have been widely used in clinical practice in China and many other regions for thousands of years. Nowadays TCD’s bioactive ingredients and mechanisms of action are being identified. However, the lack of standardized terminologies or ontologies for the description of TCDs has hindered the interoperability and deep analysis of TCD knowledge and data. By aligning with the Basic Formal Ontology (BFO), an ISO-approved top-level ontology, we constructed a community-driven TCD ontology (TCDO) with the aim of supporting standardized TCD representation and integrated analysis. TCDO provides logical and textual definitions of TCDs, TCD categories, and the properties of TCDs (i.e., nature, flavor, toxicity, and channel tropism). More than 400 popular TCD decoction pieces (TCD-DPs) and Chinese medicinal materials (CMMs) are systematically represented. The logical TCD representation in TCDO supports computer-assisted reasoning and queries using tools such as Description Logic (DL) and SPARQL queries. Our statistical analysis of the knowledge represented in TCDO revealed scientific insights about TCDs. A total of 36 TCDs with medium or high toxicity are most densely distributed, primarily in Aconitum genus, Lamiids clade, and Fabids clade. TCD toxicity is mostly associated with the hot nature and pungent or bitter flavors and has liver, kidney, and spleen channel tropism. The three pairs of TCD flavor-nature associations (i.e., bitter-cold, pungent-warm, and sweet-neutral) were identified. The significance of these findings is discussed. TCDO has also been used to support the development of a web-based traditional Chinese medicine semantic annotation system that provides comprehensive annotation for individual TCDs. As a novel formal TCD ontology, TCDO lays out a strong foundation for more advanced TCD studies in the future.

Costa Rica Central Valley gastronomic lexicon structuring from an ontological arrangement

This paper describes how terminology and ontologies interact in a coherent and exhaustive manner, and how the neological appearance is obtained from the derivation of the specificity and functionality of a specific corpus. This research shows categories that do not exist either in the Glossary of Costa Rican popular cuisine (SEDÓ MASÍS, 2008), or in the Dictionary of Costarriquenismos (QUESADA PACHECO, 2012). The omission of some of these categories clearly shows that the terms have been historically organized taking into account only the lexical factor, but not the conceptual organization. Therefore, this study intends to play with the "disagreement" between speakers and specialists to show that a reorganization of the terms of an area is possible. For this, a corpus of 596 recipes and 4652 ingredients for ontological representation was compiled. Each ontological class was defined by means of its functionality in the recipes. The ontological architecture is formalized through the postulates of Basic Formal Ontology (SMITH, 2014) and is schematized by means of Protégé. In addition, the terminological theories of Cabré (1999), Fedor de Diego (1995) and Roche (2007, 2009) are used.

Data Integration in the Brazilian Public Health System for Tuberculosis: Use of the Semantic Web to Establish Interoperability

Background Interoperability of health information systems is a challenge due to the heterogeneity of existing systems at both the technological and semantic levels of their data. The lack of existing data about interoperability disrupts intra-unit and inter-unit medical operations as well as creates challenges in conducting studies on existing data. The goal is to exchange data while providing the same meaning for data from different sources. Objective To find ways to solve this challenge, this research paper proposes an interoperability solution for the tuberculosis treatment and follow-up scenario in Brazil using Semantic Web technology supported by an ontology. Methods The entities of the ontology were allocated under the definitions of Basic Formal Ontology. Brazilian tuberculosis applications were tagged with entities from the resulting ontology. Results An interoperability layer was developed to retrieve data with the same meaning and in a structured way enabling semantic and functional interoperability. Conclusions Health professionals could use the data gathered from several data sources to enhance the effectiveness of their actions and decisions, as shown in a practical use case to integrate tuberculosis data in the State of São Paulo.