Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

Foundational Ontologies meet Ontology Matching: A Survey

Ontology matching is a research area aimed at finding ways to make different ontologies interoperable. Solutions to the problem have been proposed from different disciplines, including databases, natural language processing, and machine learning. The role of foundational ontologies for ontology matching is an important one. It is multifaceted and with room for development. This paper presents an overview of the different tasks involved in ontology matching that consider foundational ontologies. We discuss the strengths and weaknesses of existing proposals and highlight the challenges to be addressed in the future

Towards Improving Phenotype Representation in OWL

BACKGROUND: Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. METHODS: We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. RESULTS: In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. CONCLUSION: Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions

An ontology-based approach to knowledge representation for Computer-Aided Control System Design

P. 107-125Different approaches have been used in order to represent and build control engineering concepts for the computer. Software applications for these fields are becoming more and more demanding each day, and new representation schemas are continuously being developed. This paper describes a study of the use of knowledge models represented in ontologies for building Computer Aided Control Systems Design (CACSD) tools. The use of this approach allows the construction of formal conceptual structures that can be stated independently of any software application and be used in many different ones. In order to show the advantages of this approach, an ontology and an application have been built for the domain of design of lead/lag controllers with the root locus method, presenting the results and benefits found

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

ROMULUS: a Repository of Ontologies for MULtiple USes populated with foundational ontologies

A foundational ontology contributes to ontology-driven conceptual data modelling and is used to solve interoperability issues among domain ontologies. Multiple foundational ontologies have been developed in recent years, and most of them are available in several versions. This has re-introduced the interoperability problem, increased the need for a coordinated and structured comparison and elucidation of modelling decisions, and raised the requirement for software infrastructure to address this. We present here a basic step in that direction with the Repository of Ontologies for MULtiple USes, ROMULUS, which is the first online library of machine-processable, modularised, aligned, and logic-based merged foundational ontologies. In addition to the typical features of a model repository, it has a foundational ontology recommender covering features of six foundational ontologies, tailor-made modules for easier reuse, and a catalogue of mappable and non-mappable elements among the BFO, GFO and DOLCE foundational ontologies