Definition Of Ontology Research Articles

Spinoza's Definition Of Attribute: An Interpretation

Since it has generally been accepted that to Spinoza attributes are real features of substance, the interpretation of his attribute definition has become a notorious problem. The reason is that interpreters have failed to see that the definition formulates a purely epistemological account of the state of affairs. The article presents and justifies such an interpretation. It will be shown that the definition in spite of its epistemological character implies a real ontological definition, which specifies the critical features of an attribute. As to the reason why Spinoza has stated the definition in an ‘indirect way’, it is shown that it is likely that he has done so in order to have a more efficient, a more unambiguous and a more elegant definition. The relevance of the new interpretation is not only that it provides us with an interpretable, transparent attribute definition, but it also contributes to the establishment of a coherent picture of Spinoza’s metaphysics around this definition.

ONTO-PDM: Product-driven ONTOlogy for Product Data Management interoperability within manufacturing process environment

This paper proposes an approach for facilitating systems interoperability in a manufacturing environment. It is based on the postulate that an ontological model of a product may be considered as a facilitator for interoperating all application software that share information during the physical product lifecycle. The number of applications involved in manufacturing enterprises may in fact refer to the knowledge that must be embedded in it, appropriately storing all its technical data based on a common model. Standardisation initiatives (ISO and IEC) try to answer the problem of managing heterogeneous information scattered within organizations, by formalising the knowledge related to product technical data. The matter of this approach is to formalise all those technical data and concepts contributing to the definition of a Product Ontology, embedded into the product itself and making it interoperable with applications, thus minimising loss of semantics.

Interoperability through ontologies

In this paper we concentrate on facilitating and quickening mutual communications between several systems thus allowing their closely interconnection, alias interoperability. We discuss wide definition of word ontology and describe sets of criteria and properties that help us divide ontologies. For presentation of so far discovered ways of ontology utilization for our purposes we describe several model applications that help closer understanding and classifying of ontology applications. We split described applications into two categories: information purvey and mutual access to knowledge.

Bootstrapping Ontologies for Web Services

Ontologies have become the de-facto modeling tool of choice, employed in many applications and prominently in the semantic web. Nevertheless, ontology construction remains a daunting task. Ontological bootstrapping, which aims at automatically generating concepts and their relations in a given domain, is a promising technique for ontology construction. Bootstrapping an ontology based on a set of predefined textual sources, such as web services, must address the problem of multiple, largely unrelated concepts. In this paper, we propose an ontology bootstrapping process for web services. We exploit the advantage that web services usually consist of both WSDL and free text descriptors. The WSDL descriptor is evaluated using two methods, namely Term Frequency/Inverse Document Frequency (TF/IDF) and web context generation. Our proposed ontology bootstrapping process integrates the results of both methods and applies a third method to validate the concepts using the service free text descriptor, thereby offering a more accurate definition of ontologies. We extensively validated our bootstrapping method using a large repository of real-world web services and verified the results against existing ontologies. The experimental results indicate high precision. Furthermore, the recall versus precision comparison of the results when each method is separately implemented presents the advantage of our integrated bootstrapping approach.

Signs and terminology: Science caught between language and perception

After briefly discussing various problems that can result from linguistic ambiguities, I attempt to provide an introduction and overview of various aspects and theories that are relevant to scientific terminology. These include a general semiotics (i.e., theory of signs), the distinction of semantic conceptual content and aesthetic nonconceptual content and their relationship to each other, a discussion of different types of scientific concepts (e.g., essentialistic and cluster classes, natural kinds, type approach), and the importance of specifying epistemological recognition criteria for empirical concepts in addition to their ontological theoretical definitions and the specification of contexts in which the concepts are used and on which theories they depend upon. I then provide a distinction of raw data, data, metadata, information and knowledge, and discuss the relation between images and data and how efforts to standardize data and metadata can affect scientific terminology. I briefly introduce new methods and techniques for increasing semantic transparency and communicability in science, which include the organization and the management of scientific terms within taxonomies, and their formal representation in ontologies. The usefulness of terminological standardization and its possible negative effects on scientific progress is then discussed, and finally the question is addressed of whether one can distinguish types of terminologies that benefit from standardization from those that could suffer from it.

War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

The use of structured knowledge representations—ontologies and terminologies—has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.

Automating generation of textual class definitions from OWL to English

BackgroundText definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable effort and there is often a lag between specification of the main part of an ontology (logical descriptions and definitions of entities) and the development of the text-based definitions. The goal of natural language generation (NLG) from ontologies is to take the logical description of entities and generate fluent natural language. The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand.ResultsTo produce the descriptions, the program collects all the axioms relating to a given entity, groups them according to common structure, realises each group through an English sentence, and assembles the resulting sentences into a paragraph, to form as ‘coherent’ a text as possible without human intervention. Sentence generation is accomplished using a generic grammar based on logical patterns in OWL, together with a lexicon for realising atomic entities. We have tested our output for the Experimental Factor Ontology (EFO) using a simple survey strategy to explore the fluency of the generated text and how well it conveys the underlying axiomatisation. Two rounds of survey and improvement show that overall the generated English definitions are found to convey the intended meaning of the axiomatisation in a satisfactory manner. The surveys also suggested that one form of generated English will not be universally liked; that intrusion of too much ‘formal ontology’ was not liked; and that too much explicit exposure of OWL semantics was also not liked.ConclusionsOur prototype tools can generate reasonable paragraphs of English text that can act as definitions. The definitions were found acceptable by our survey and, as a result, the developers of EFO are sufficiently satisfied with the output that the generated definitions have been incorporated into EFO. Whilst not a substitute for hand-written textual definitions, our generated definitions are a useful starting point.AvailabilityAn on-line version of the NLG text definition tool can be found at http://swat.open.ac.uk/tools/. The questionaire and sample generated text definitions may be found at http://mcs.open.ac.uk/nlg/SWAT/bio-ontologies.html.

Ontology definition and construction, and epistemological adequacy for systems interoperability: A practitioner analysis

Ontology development is considered to be a useful approach to the design and implementation of interoperable systems. This literature review and commentary examines the current state of knowledge in this field with particular reference to processes involved in assuring epistemological adequacy. It takes the perspective of the information systems practitioner keen to adopt a systematic approach to in-house ontology design, taking into consideration previously published work. The study arises from author involvement in an integration/interoperability project on systems that support Scottish Common Housing Registers in which, ultimately, ontological modelling was not deployed. Issues concerning the agreement of meaning, and the implications for the creation of interoperable systems, are discussed. The extent to which those theories, methods and frameworks provide practitioners with a usable set of tools is explored, and examples of practical applications of ontological modelling are noted. The findings from the review of the literature demonstrate a number of difficulties faced by information systems practitioners keen to develop and deploy domain ontologies. A major problem is deciding which broad approach to take: to rely on automatic ontology construction techniques, or to rely on keywords and domain experts to develop ontologies.

A new process-based ontology for KBE system implementation: application to inspection process planning

This paper focuses in the definition of a new ontology (Onto-Process) and the resulting informal model. The developed ontology constitutes an improvement to other ontologies since it covers the requirements of manufacturing processes engineering and, in particular, the inspection planning process with automated machines. Inspection planning activity usually implies to make repetitive and well-known decisions. These decisions are often based on the knowledge of inspection operators; therefore, it is a good candidate for implementing a knowledge-based engineering system. The sequence of activities involved in the inspection planning has been identified using Icam definition diagrams (IDEF0) in order to express the knowledge at a high level. These diagrams constitute an important support for defining the sequence of activities and the information flow. Later on, this information has been analyzed in depth using conceptual maps and it has been classified into units of knowledge. Then, each of these units of knowledge is decomposed into elementary objects of knowledge and relationships among them are defined. In a first approach, the ontology has been tested using a very particular but essential task in inspection planning: the activity related to the definition of contact points over inspection surfaces. In this activity, decisions must be made about the number, distribution, and sequencing of points. In the methodology developed in this paper the differences between form and non-form error inspection is considered. Finally, the knowledge required to support these decisions is represented using Onto-Process.

Searching biosignal databases by content and context: Research Oriented Integration System for ECG Signals (ROISES)

Technological advances in textile, biosensor and electrocardiography domain induced the wide spread use of bio-signal acquisition devices leading to the generation of massive bio-signal datasets. Among the most popular bio-signals, electrocardiogram (ECG) possesses the longest tradition in bio-signal monitoring and recording, being a strong and relatively robust signal. As research resources are fostered, research community promotes the need to extract new knowledge from bio-signals towards the adoption of new medical procedures. However, integrated access, query and management of ECGs are impeded by the diversity and heterogeneity of bio-signal storage data formats. In this scope, the proposed work introduces a new methodology for the unified access to bio-signal databases and the accompanying metadata. It allows decoupling information retrieval from actual underlying datasource structures and enables transparent content and context based searching from multiple data resources. Our approach is based on the definition of an interactive global ontology which manipulates the similarities and the differences of the underlying sources to either establish similarity mappings or enrich its terminological structure. We also introduce ROISES (Research Oriented Integration System for ECG Signals), for the definition of complex content based queries against the diverse bio-signal data sources.

The Anxiety of Authenticity in Dahan's La Vie En Rose and Zeffirelli's Callas Forever

Two musical biographical pictures, Olivier Dahan's La Vie En Rose (2007) and Franco Zeffirelli's Callas Forever (2002) address various ways the seemingly decisive, yet ever elusive, problem of authenticity. How should we define authenticity, and how can one account for the near hysteria surrounding the desire to achieve it, particularly cinema? (1) According to The Oxford English Dictionary, authenticity is a quality that is in accordance with fact, ... true substance as well as first hand as opposed to copied.(2) Emulating the platonic gesture that distinguishes between model and copy, authenticity presents itself as an original, yet doing so, paradoxically refers to a preexisting model, therefore already blurring the borders between the copy and the real thing. More interesting than trying to establish an ontological definition of authenticity is what the desire for authenticity, which implies a perceived lack thereof, betrays. In fact, the obsession with authenticity cinema appears to be the symptom of a modern nostalgia for some paradise lost, the longing for a time when life was transparent and free of the modern apparatuses separating us from the world, turning reality not even into a theater stage, but into a movie theater, the most mediated, and therefore, artificial, of all representations. In the age of social mobility, globalization, and, most of all, the mechanical reproduction of the work of art, the search for authenticity seems to have become increasingly pressing, particularly as related to the art of illusion that is cinema. Mixing two hybrid and somewhat incompatible genres, the musical comedy and the melodramatic biopic, both films covered this analysis wrestle with different kinds of authenticity that constantly attempt to distance themselves from their supposed opposite, artificiality. In relation to these two specific films, the issue of authenticity, or rather, the issue of authenticity being an issue, is explored on three different planes: narrative, genre, and medium. In each section, this essay will seek to explore why these films so desperately strive for authenticity, and how they go about convincing the audience they have achieved it. This essay begins by focusing on narrative authenticity, which helps the audience locate stable aesthetic and moral essences through romantic tropes and a melodramatic mode. This analysis then explores genre authenticity, investigating why it seems particularly important to these musical biopics to come off as authentic, and how they attempt to do so by (re)defining the categories of the musical comedy, the musical biopic and the biopic. If authenticity a musical comedy is generally characterized by balance, with the integration of the music within the narrative and of the singer within the ensemble cast, then the imbalance of the musical biopic, with its emphasis on musical numbers and a single protagonist, implicitly disrupts the very category of generic authenticity. Furthermore, if authenticity a biographical work seems to refer straight back to a historical truth, the biopic liberally mixes fiction and nonfiction, thereby crossing repeatedly over the boundaries between history and fantasy. Finally, this essay examines medium authenticity, i.e. the many ways which the musical biopic anxiously hides its inauthentic alienated nature by trying to create the illusion of life through performance. Here, authenticity serves to deliver the (inevitably mediated) immediacy which nostalgic filmgoers crave. Narrative Authenticity: The Biopic and Its Artist While both La Vie En Rose and Callas Forever ostensibly fit within the biopic genre, they differ critically their approach and style. La Vie En Rose tells the story of Edith Piaf (Marion Cotillard), France's most beloved popular singer from the thirties to the sixties; Callas Forever focuses on the life of Maria Callas (Fanny Ardant), the world's most renowned opera singer from the forties to the seventies. …

An inclusive ontology based on the categories of intelligent software agents: an exploratory research

The main purpose of this paper is to illustrate a pervasively explored literature-based categorisation of intelligent software agents and present a new taxonomy of them through the definition of ontology for helping and guiding the future research, both in theory and practice, toward coherence. The process of category building has undergone a broad literature review of various related papers and academic works. The aim of the categorisation has been the extraction of an encompassing ontology which covers a wide range of internationally accepted types of agents and their corresponding features in order for the researchers to apply them into the appropriate context as required. Such ontology considerably helps the academic scholars in developing the related literature based on the firm ground provided and it will also contribute to the practitioners in developing multi-agent systems based on the similarities, differences, and cross-functional features and characteristics of intelligent software agents provided in the ontology of agent categories and features.

Unlocking Data for Clinical Research – The German i2b2 Experience

Data from clinical care is increasingly being used for research purposes. The i2b2 platform has been introduced in some US research communities as a tool for data integration and querying by clinical users. The purpose of this project was to assess the applicability of i2b2 in Germany regarding use cases, functionality and integration with privacy enhancing tools. A set of four research usage scenarios was chosen, including the transformation and import of ontology and fact data from existing clinical data collections into i2b2 v1.4 instances. Query performance was measured in comparison to native SQL queries. A setup and administration tool for i2b2 was developed. An extraction tool for CDISC ODM data was programmed. Interfaces for the TMF privacy enhancing tools (PID Generator, Pseudonymization Service) were implemented. Data could be imported in all tested scenarios from various source systems, including the generation of i2b2 ontology definitions. The integration of TMF privacy enhancing tools was possible without modification of the platform. Limitations were found regarding query performance in comparison to native SQL and certain temporal queries. i2b2 is a viable platform for data query tasks in use cases typical for networked medical research in Germany. The integration of privacy enhancing tools facilitates the use of i2b2 within established data protection concepts. Entry barriers should be lowered by providing tools for simplified setup and import of medical standard formats like CDISC ODM.

Is neuroeconomics doomed by the reverse inference fallacy?

Neuroeconomic studies are liable to fall into the reverse inference fallacy, a form of affirmation of the consequent. More generally neuroeconomics relies on two problematic steps, namely the inference from brain activities to the engagement of cognitive processes in experimental tasks, and the presupposition that such inferred cognitive processes are relevant to economic theorizing. The first step only constitutes the reverse inference fallacy proper and ways to correct it include a better sense of the neural response selectivity of the targeted brain areas and a better definition of relevant cognitive ontologies for neuroeconomics. This second way also allows increased coherence between the cognitive processes actually involved in neuroeconomics experiments and the theoretical constructs of economics. We suggest means of increasing neural response selectivity in neuroeconomic experimental paradigms. We also discuss how the choice of cognitive ontologies can both avoid implicit reductionist strategies (from economic constructs to neural patterns) and irrelevance, as cognitive processes engaged in experimental tasks may lack immediate bearing on the study of economic behavior. With these joint improvements neuroeconomics can be a progressive science.

Ontology Modeling Profile , an Extension for the Ontology UML Profile

paper presents an extension for the Ontology Modeling Profile (OUP). The extended profile together with Ontology Definition Metamodel (ODM), enables the usage of Model Driven Architecture (MDA) standards in ontological engineering. Our profile is based on the recent W3C effort - The Web Ontology Language (OWL). We have shown the role of individuals and slots in building OWL statements. This utilization improves the practical implementation of Ontology models using UML profiles..

Model Transformation from Ontology Model to Content Analysis Model

This paper introduces a technique to extend existing Web engineering methodologies to develop the semantic web applications. We investigate the use of ontology in the domain analysis for the development of web applications. The contribution of this paper is the automatic generation of Content Analysis Model from the Ontology Model. This technique makes a straight forward mapping between Ontology Definition Metamodel (ODM) model’s elements and the Content Analysis Model’s elements. We further show how this technique could be integrated with many web engineering methodologies, which are based on systematic and automatic chain of transformation during all the development phases. The requirement model that is generated from the Ontology model guarantees that an application terminologies are unified all over the web engineering process.

Ontology-based simulation in agricultural systems modeling

A methodology and applications of ontology-based simulation are presented. An environment for building simulations based on the Lyra ontology management system is described which includes web-based visual design tools for constructing models and automatically generating simulation code. The ontology is used for representing all equations and all symbols appearing in these equations that are needed to describe a model. The example applications presented are models of soil, water, and nutrient management in citrus and sugarcane. Results thus far show that the ontology-based approach has advantages for representing the model structure, equations, and symbols, that complex models can be described in this format, and that efficient simulation code can be generated automatically from the ontology definition of the model. Potential applications, not yet fully explored, include ability to automatically connect models and data sources, using the ontology to organize model bases containing many models and model components, and using ontology reasoners to search for models, automatically discover model similarities and differences, and generate model instances from general principles.

An Introduction to Knowledge Representation and Ontology Development for Systems Engineers

AbstractEffective communication requires a common vocabulary. An ontology provides a description of the terminology, concepts and relationships for a particular area of interest. An ontology may be viewed as a declarative encoding of the meaning of the domain vocabulary terms, thus making it a key to enabling communication. For systems that are used by people whose understanding of a domain is not necessarily consistent, an explicit description of the important terms can be extremely useful.Many commercial companies have successfully deployed applications with increasing use of semantics such as taxonomy‐based search and navigation services. Rule‐based manufacturing, product configuration, and financial services systems have been relatively common in those industries for many years. Fewer organizations have successfully deployed semantically rich systems that incorporate ontology‐based metadata, sophisticated reasoning and explanation support. The technology has been around for decades, though its use for web‐based applications is relatively recent, and it remains difficult for some people to understand, let alone use effectively.This tutorial provides an overview of the knowledge representation landscape and attempts to demystify some of the “black art” of ontology development. We will outline basic methodology steps developed from a combination of Domain analysis methodology from software engineering IDEF methods developed for the US Department of Defense Best practices developed through extensive experience and lessons learned, with a focus on problems in software and systems engineering Examples from systems engineering will be provided, with emphasis on ontology development in UML using the Ontology Definition Metamodel, applications that lend themselves to vocabulary development in the Web Ontology Language (OWL), and use of the these technologies together with models developed using the OMG's Systems Modeling Language (SysML).

O papel das definições na pesquisa em ontologia

Investiga o uso de definição como um fator importante para a expressividade semântica em ontologias. Estudos revelam que as ontologias atuais não possuem padrão para definições. Isso levanta a questão de compatibilidade entre vocabulários que operam em bases cooperativas, como é o caso das pesquisas desenvolvidas em Bioinformática. A literatura tem apresentado alguma discussão em torno das definições em ontologias, mas principalmente como uma análise das definições existentes. Baseada em princípios teóricos, esta pesquisa visa desenvolver um tipo adequado de definição para a construção de ontologias de domínio consistente, ou seja, as definições operacionais.

Anomalies in ontologies with rules

For the development of practical semantic applications, ontologies are commonly used with rule extensions. Prominent examples of semantic applications not only are Semantic Wikis, Semantic Desktops, but also advanced Web Services and agents. The application of rules increases the expressiveness of the underlying knowledge in many ways. Likewise, the integration not only creates new challenges for the design process of such ontologies, but also existing evaluation methods have to cope with the extension of ontologies by rules. Since the verification of Owl ontologies with rule extensions is not tractable in general, we propose to verify ontologies at the symbolic level by using a declarative approach: With the new language Datalog ⋆, known anomalies can be easily specified and tested in a compact manner. We introduce supplements to existing verification techniques to support the design of ontologies with rule enhancements, and we focus on the detection of anomalies that especially occur due to the combined use of rules and ontological definitions.