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Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration.
Abstract
Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C's LinkSuiteTM with the philosophical rigor of IFOMIS's Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date.
... Ontology According to Gruber (1993) an ontology is an explicit specification of a conceptualization. However, the ontology of the H14 topic map aims to go beyond a mere conceptualization and rather subscribes to the realistic approach advocated by Fielding et al. (2004) who stated: In his Physics , Aristotle writes, 'When the objects of an inquiry, in any department, have principles, conditions, or elements, it is through acquaintance with these that knowledge, that is to say scientific knowledge, is attained,' and we would do well to keep such words in mind today when we seek to design an adequate inventory of ontological elements for database integration and navigation. ...
... We aimed for a realistic ontological approach as advocated by Fielding et al. (2004), rooted in high level universals such as object, process, method, and property. For linking these high level universals to the low level universals characterizing the entities dealt with at the laboratory level, we used the superclass-subclass relation. ...
In the EU Waste Ring test 2006/2007 a very high number of reference tests were performed for three standard (Algae, Daphnia and Luminescent bacteria) as well as various additional (Lemna, Brachyonus, Ceriodaphnia, and Pseudomonas) test systems. These results were required by the respective test guidelines to prove the sensitivity of the test organisms.
In addition, tests with two reference substances provided results confirming the validity of the umu tests performed. Besides
the required reference substances, in some tests additional chemicals were tested. The number of the required reference tests,
mainly potassium dichromate in the standard tests, was so high that these results could be used for the re-evaluation of the
data ranges listed in the test guidelines. The range given in the current Algae test guideline, based on old ring test data,
should be changed and so a new range is proposed here. In the additional tests, the number of data sets provided, often with
different reference substances, was much lower. Since potassium dichromate did not cause problems in the various tests, it
is recommended that this substance be used as the standard reference substance in aquatic tests.
... Ontology According to Gruber (1993) an ontology is an explicit specification of a conceptualization. However, the ontology of the H14 topic map aims to go beyond a mere conceptualization and rather subscribes to the realistic approach advocated by Fielding et al. (2004) who stated: In his Physics , Aristotle writes, 'When the objects of an inquiry, in any department, have principles, conditions, or elements, it is through acquaintance with these that knowledge, that is to say scientific knowledge, is attained,' and we would do well to keep such words in mind today when we seek to design an adequate inventory of ontological elements for database integration and navigation. ...
... We aimed for a realistic ontological approach as advocated by Fielding et al. (2004), rooted in high level universals such as object, process, method, and property. For linking these high level universals to the low level universals characterizing the entities dealt with at the laboratory level, we used the superclass-subclass relation. ...
The statistical evaluation of the ring test data (only standard test battery) was performed in a step-wise process. First,
the individual test results (EC/LC50 values) were recalculated (using probit analysis and the ToxRat program). Secondly, they had to fulfil several acceptance
criteria. Data sets which passed these acceptance criteria were evaluated in two different ways in parallel: according to
the approach usually used for the validation of chemical and physicochemical methods in environmental analysis (ISO 5725-2
(2002)) and according to the warning limit approach following Environment Canada (2005). However, for the evaluation of the
results from ecotoxicological tests, the ISO approach had to be modified. Assuming that EC/LC50 values are log-normally distributed, the log-transformed EC/LC50 values were used instead of the original EC/LC50 values, to calculate means and standard deviations. Hence the re-transformed total means are not arithmetic but geometric
means. Since the ecotoxicological test procedures in question are tedious and elaborate compared with trace analytical investigations,
replicate determinations within a given laboratory and within short intervals of time were impossible. Thus, repeatability
and reproducibility were evaluated using the results of the different laboratories together with the confidence intervals
of the results, which were each calculated by application of the same algorithm. In addition, the results of the individual
tests were used to calculate warning limits according to Environment Canada (2005). The test results that were identified
as statistical outliers (ISO approach) or those outside the warning limits (Environment Canada) were excluded from the calculation
of the final geometrical mean EC/LC50. As a measure of robustness, the ratio between reproducibility and repeatability standard deviation, the standard deviations
calculated according to the warning limit approach and the factor between minimum and maximum EC/LC50 value are presented. Finally, recommendations to improve the statistical evaluation of data from ecotoxicological ring tests
are given.
... Ontology According to Gruber (1993) an ontology is an explicit specification of a conceptualization. However, the ontology of the H14 topic map aims to go beyond a mere conceptualization and rather subscribes to the realistic approach advocated by Fielding et al. (2004) who stated: In his Physics , Aristotle writes, 'When the objects of an inquiry, in any department, have principles, conditions, or elements, it is through acquaintance with these that knowledge, that is to say scientific knowledge, is attained,' and we would do well to keep such words in mind today when we seek to design an adequate inventory of ontological elements for database integration and navigation. ...
... We aimed for a realistic ontological approach as advocated by Fielding et al. (2004), rooted in high level universals such as object, process, method, and property. For linking these high level universals to the low level universals characterizing the entities dealt with at the laboratory level, we used the superclass-subclass relation. ...
Earthworms are considered an important part of the soil community, so they represent soil organisms in the test set for the
ecotoxicological characterization of wastes. In keeping with the ISO standard guideline 11268-1, the acute earthworm test
was performed with three waste types: INC, SOI, and WOO. A total of 44 tests out of the 52 tests conducted were classified
as acceptable. Methodologically, almost no problems occurred, but further guidelines on determining the moisture of the test
substrate mixtures are needed. After statistical evaluation, only one other test result was rejected. The min-max factors
(2–5) between individual LC50 values and the CVs (20–31%) were low, showing that the acute earthworm test is a robust method. Toxicity differed considerably
between the three waste types, as seen in the final LC50 values: INC = 46.3%, SOI ³ 50%, WOO = 21.0%. These results are in agreement with the few data known from the literature.
The sensitivity of the earthworm acute test was low compared to other plant and invertebrate tests with solid wastes. Therefore,
it is recommended that a more sensitive alternative be found: either an earthworm test with a chronic endpoint such as reproduction,
or another invertebrate species (e.g. a collembolan) should replace this test. In addition, an alternative for the currently
used reference substance chloroacetemide (boric acid) should be selected.
Keywords
Eisenia fetida/andrei
-Acute test-Ring test-Waste-Ash-Wood-PAH
... This approach treats perdurants as if they are endurants, but this objectification does not solve the connection between endurants and perdurants . For example, if one wants to couple some biological process with a cellular component, new relationships between the two ontologies need to be created (e.g. [5]). Thus, adding new knowledge about the combination that may result in a separate new 'situation ontology', or a mapping ontology that is positioned between BP and CC. ...
... Perdurants include types of entities such as processes, events and states, in contrast with modeling paradigms in informatics and most ontological investigations, where the center of attention is the entity of the thing-quality paradigm. Philosophically, there are arguments for and against such emphasis: processes can only exist when there are endurants that are the 'carriers' of the process [5]. On the other hand, objects only come into existence through a process (refer to [6] and [7] for a wider scope of arguments). ...
Few ontologies in the ecological domain exist, but their development can take advantage of gained experience in other domains and from existing modeling practices in ecology. Taxonomies do not suffice because more expressive modeling techniques are already available in ecology, and the perspective of flow with its centrality of events and processes cannot be represented adequately in a taxonomy. Therefore, formal ontologies are required for sufficient expressivity and to be of benefit to ecologists, which also enables future reuse. We have created a formal mapping between the software-supported ecological modeling method and software tool STELLA and ontology elements, which simplifies bottom-up ontology development considerably and has excellent potential for semi-automated ontology development. However, the conducted experiments also revealed that ontology development for ecology is close to being part of ecological research that through the formalized representation of the knowledge more clearly points to lacunas and suggestions for further research in ecology.
... Each repository could be queried either using unified, higher-level concepts referring to common-use cerebrovascular phenotypes, or using new, user-defined phenotypes, assembled from elementary phenotype units. To achieve this goal, we developed an ontological model [26][27][28][29][30] for cerebrovascular phenotypes -the NEUROWEB Reference Ontology -that accurately captures the core diagnostic/classificatory knowledge of clinicians. The development of the Reference Ontology required very intensive knowledge acquisition and knowledge structuring activities, leading to a progressive refinement of the semantic model, as described in Section 2. In the final model, top-level diagnostic classes are deconstructed into more elementary phenotypes and medical concepts. ...
... An additional dimension to be taken into account is the anatomical location implied by the phenotype. Anatomical parts cannot be regarded as phenotypes (i.e., observable properties): they are rather physical entities bearing observable properties [29][30][31]33]. For this reason, we introduced new types of entities, Anatomical Parts and Topological Concepts. ...
The NEUROWEB project supports cerebrovascular researchers' association studies, intended as the search for statistical correlations between a feature (e.g., a genotype) and a phenotype. In this project the phenotype refers to the patients' pathological state, and thus it is formulated on the basis of the clinical data collected during the diagnostic activity. In order to enhance the statistical robustness of the association inquiries, the project involves four European Union clinical institutions. Each institution provides its proprietary repository, storing patients' data. Although all sites comply with common diagnostic guidelines, they also adopt specific protocols, resulting in partially discrepant repository contents. Therefore, in order to effectively exploit NEUROWEB data for association studies, it is necessary to provide a framework for the phenotype formulation, grounded on the clinical repository content which explicitly addresses the inherent integration problem. To that end, we developed an ontological model for cerebrovascular phenotypes, the NEUROWEB Reference Ontology, composed of three layers. The top-layer (Top Phenotypes) is an expert-based cerebrovascular disease taxonomy. The middle-layer deconstructs the Top Phenotypes into more elementary phenotypes (Low Phenotypes) and general-use medical concepts such as anatomical parts and topological concepts. The bottom-layer (Core Data Set, or CDS) comprises the clinical indicators required for cerebrovascular disorder diagnosis. Low Phenotypes are connected to the bottom-layer (CDS) by specifying what combination of CDS values is required for their existence. Finally, CDS elements are mapped to the local repositories of clinical data. The NEUROWEB system exploits the Reference Ontology to query the different repositories and to retrieve patients characterized by a common phenotype.
... From this point of view, the user feels a need for bi-directed relationships among these databases and the concepts within them. Generally, design and implementation of separated and heterogeneous databases cause many problems and challenges during the communication phase of these systems [2, 3]. In the last two decades, there were many approaches to solve the semantic inconsistencies among the relational databases. ...
Integrating heterogeneous data in distributed
databases has been a research issue for many years. In
this paper, we discuss some of these problems and propose
a solution using a semantic model. This semantic
model is built upon the semantic relationships between
existing data. Applying these semantics enables us to take
into account different dimensions of user queries and find
the best possible answer for them. The proposed approach
leads us to introducing "a common language that is understandable
for all databases". We use such a common language
in order to return an effective response to the user’s
query, as well as reducing the problems of integration.
... According to Guizzardi et al. [9], the use of foundational concepts that take truly ontological issues seriously is becoming more and more accepted in the ontological engineering literature. In addition, the authors state that, in order to represent a complex domain, one should rely on engineering tools (e.g., design patterns), modeling languages, and methodologies that are based on well-founded ontological theories in the philosophical sense (see [17,18], for instance). Especially in complex domains – i.e., domains with complex concepts, relations, and constraints – and in domains with potentially serious risks of interoperability problems (the domain specified in the ITU-T Recommendation G.805 fits in both cases), a supporting ontology engineering approach should be able to: a. allow the conceptual modelers and domain experts to be explicit, regarding their ontological commitments, which enables them to expose subtle distinctions between models to be integrated and to minimize the chances of running into a False Agreement Problem [19]; b. support the user in justifying their modeling choices and providing a sound design rationale for choosing how the elements in the universe of discourse should be modeled in terms of language elements [9]. ...
Standards are documents that aim to define norms and common understanding of a subject by a group of people. In order to accomplish this purpose, these documents must define its terms and concepts in a clear and unambiguous way. Standards can be written in two different ways: by informal specification (e.g. natural language) or formal specification (e.g. math-based languages or diagrammatic ones). Remarkable papers have already shown how well-founded ontology languages provide resources for the specification’s author to better distinguish concepts and relations meanings, resulting in a better specification. This paper has the objective to expose the importance of truly ontological distinctions for standardizations. To achieve this objective, we evaluate a math-based formal specification, in Z notation, using a well-founded ontology language for a telecommunications case study, the ITU-T Recommendation G.805. The results confirm that truly ontological distinctions are essential for clear and unambiguous specifications.
... In the top-down approach to ontology development, ontology designers also start with the [Fielding et. al., 2004]. None of these upper level ontologies constitutes an ideal representation of the world -and perhaps we will never have a perfect one. Therefore, an ontology engineer has to make a compromise between the imperfection of the model representation, and one's practical needs. DOLCE has a cognitive bias. It aims to represent major classes fo ...
... Additionally, in the coming era of Internet of Things, a formal machine readable presentation of knowledge increases significantly and even becomes critically important for building a global platform containing Knowledge, Social and Business information. There are a number of papers which consider Ontology as a general approach in achieving this goal [9][10][11]. The aim of this paper is to illustrate an Ontology-oriented approach for Ecology knowledge and a more specific formal presentation of the Plant Functional Type applying engineering approach and RDF/OWL schema languages. ...
The application of Ontologies in the description of biology has become widely spread. This paper presents an approach for the application of Ontology in the description of complex ecological categories as Plant Functional Types. The authors illustrate the application of two Ontology approaches of engineering - usage of Unified Modelling Language and Semantic Web approach - usage of RDF/OWL schema languages. Both approaches are powerful enough to be used as tools for formal description and information dissemination of complex ecological categories. The conversion of both approaches in general is under development in the Object Management Group (OMG).
... Additionally, in the coming era of Internet of Things, a formal machine readable presentation of knowledge increases significantly and even becomes critically important for building a global platform containing Knowledge, Social and Business information. There are a number of papers which consider Ontology as a general approach in achieving this goal [9][10][11]. The aim of this paper is to illustrate an Ontology-oriented approach for Ecology knowledge and a more specific formal presentation of the Plant Functional Type applying engineering approach and RDF/OWL schema languages. ...
The application of Ontologies in the description of biology has become widely spread. This paper presents an approach for the application of Ontology in the description of complex ecological categories as Plant Functional Types. The authors illustrate the application of two Ontology approaches of engineering – usage of Unified Modelling Language and Semantic Web approach – usage of RDF/OWL schema languages. Both approaches are powerful enough to be used as tools for formal description and information dissemination of complex ecological categories. The conversion of both approaches in general is under development in the Object Management Group (OMG).
... Fielding et al. and Rosse et al. warned that modelers in ontological engineering frequently try to conflate divergent perspectives on reality within a single hierarchy [28,29]. Notably, basing all representation on an agreed-upon reality can prevent this. ...
Modeling clinical processes (and their informational representation) is a prerequisite for optimally enabling and supporting high quality and safe care through information and communication technology and meaningful use of gathered information.
The paper investigates existing approaches to clinical modeling, thereby systematically analyzing the underlying principles, the consistency with and the integration opportunity to other existing or emerging projects, as well as the correctness of representing the reality of health and health services.
The analysis is performed using an architectural framework for modeling real-world systems. In addition, fundamental work on the representation of facts, relations, and processes in the clinical domain by ontologies is applied, thereby including the integration of advanced methodologies such as translational and system medicine.
The paper demonstrates fundamental weaknesses and different maturity as well as evolutionary potential in the approaches considered. It offers a development process starting with the business domain and its ontologies, continuing with the Reference Model-Open Distributed Processing (RM-ODP) related conceptual models in the ICT ontology space, the information and the computational view, and concluding with the implementation details represented as engineering and technology view, respectively.
The existing approaches reflect at different levels the clinical domain, put the main focus on different phases of the development process instead of first establishing the real business process representation and therefore enable quite differently and partially limitedly the domain experts' involvement.
... On the other hand, there are many real applications which discuss the issues of procedures for the integration of terminology systems and information systems. A methodology for developing and implementing the principles for maintaining the structure of large increasing terminology system was researched to provide a way to keep consistency between those systems and their applications [8]. The Veterans Health Administration in United States has evaluated the coverage of the SCT terms and applied it into their Information system [9]. ...
This paper identifies the underlying data model inferable from the SNOMED CT data. It describes the reverse engineering of the SCT data files to create a conceptual data model of its organisation based on its data contents, not its hypothetical design model, so as to improve the means of managing and implementing the SCT data through a conventional persistent store. This also provides some potential for re-installing SCT back into an ontological store that better suits local requirements. The analysis of the resultant data model shows the SCT does not have any integrity constraints usable within a relational database model and thereby any information systems implementation will have to create its own integrity maintenance. This creates the likelihood that differences between implementers can be expected and modifications to the SCT releases can be not be assured of consistent implementation and so threatens true interoperability between information systems.
... Ontologies are collections of concepts (universals), instances of concepts (particulars) and relations among them (Fielding et al., 2004). Attributes are assigned to concepts, instances and relations in order to specify the content of the knowledge network. ...
The cooperative and collaborative nature of healthcare delivery requires active user participation in healthcare process design/redesign. Hence, there is a need to provide users with reusable, flexible, agile and adaptable training material in order to enable them instil their knowledge and expertise in healthcare process modelling and automation activities. This paper presents a prototype approach for designing user training material which is based on externalising domain knowledge in the form of ontology-based knowledge networks. The approach provides significant advantages to both designers (knowledge-content reusability and Semantic Web enabling) and users (semantic search, knowledge navigation and knowledge dissemination).
... Hence, instead of conceiving aging as a temporal condition of human beings reificated into agents (the 'old ages'), our approach looks at aging in terms of the disposition to get aged essentially embodied into timely-based carriers (Merleau Ponty 1945). In other words, rather than to put the focus on the old ages as bearers of a momentum along the ontogenetic process of humans, we advocate the adoption of technologies that see elderly people as perdurant entities (Fielding et al., 2004) whose development unfolds in the continuum present of the life process. Present is nothing but our experience, that is, it is the incomplete texture that brings together the elapsed events with their punctual caption within an open ended reminiscence process. ...
The paper considers the case of web-based technologies that facilitate members of ad-hoc online communities in narrating either episodes from their life or the progress of their health conditions in the context of either informal/familiar relationships or more formal/professional relationships. We discuss the role that such narrative-promoting technologies can play in changing commonplace associations between the elderly and the impaired/ill, and shed light on the main tenets that can be drawn from a multidisciplinary literature on narratives for their informed design. Finally, we will make a point to advocate further research and analyses towards technologies that give users the power to create the content on which to ground meaningful and possibly empathic relationships, and by which to provide others with more faithful images of their aging and health.
... Ontologies are collections of concepts (universals), instances of concepts (particulars) and relations among them (Fielding, Simon, Ceusters, & Smith, 2004). Attributes are assigned to concepts, instances and relations in order to specify the content of the knowledge network. ...
The present paper is concerned with an ontology-based knowledge network developed for the semantic representation of the feasibility studies preparation procedure. Specifically, a training scenario in feasibility studies and business plan preparing was built, using the CULTOS tools that are based on a self-contained reusable knowledge repository, which combines the ontology constructs with supportive multimedia objects. The proposed approach may have significant impact to enabling users participate actively in the feasibility studies preparing process since they are equipped with an appropri- ate tool for acquiring a clear and an in depth understanding of this process. Through the present applica- tion, it seems that the model could combine any existing multimedia material with ontology constructs, using knowledge-based multimedia authoring tools, in order to build user-training scenarios and satisfy specific training needs.
... Top-level ontologies can be used as a formal foundation for building domain ontologies—doing so can facilitate semantic integration across ontologies at a later time. Alternatively, domain ontologies can also be built first and then linked to top-level ontologies [60,61] (Fig. 2). The fundamental ontological commitments and distinctions that are laid out in coherent top-level ontologies are part of the reason they can be useful in decision-making during ontology construction. ...
Research on ontologies is becoming widespread in the biomedical informatics community. At the same time, it has become apparent that the challenges of properly constructing and maintaining ontologies have proven more difficult than many workers in the field initially expected. Discovering general, feasible methods has thus become a central activity for many of those hoping to reap the benefits of ontologies. This paper reviews current methods in the construction, maintenance, alignment, and evaluation of ontologies.
A co-edited special volume in Cosmos+Taxis that brings together specialists in ontology, social ontology, biomedical ontology, logic, ethics, and value theory.
This paper is part of a Festschrift volume titled "Barry Smith an sich," and it employs the economic concept of sunk costs and the psychological method of mindfulness to examine the way to achieve a good life.
Smart building monitoring demands a new software infrastructure that can elaborate building domain knowledge in order to provide advanced and intelligent functionalities. Conventional facility management (FM) software tools lack semantically rich components, and that limits the capability of supporting software for automatic information sharing, resource negotiation and to assist in timely decision making. Recent hardware innovation on compact ZigBee sensor devices, software developments on ontology and intelligent software agent paradigms provide a good opportunity to develop tools that can further improve current FM practices. This paper introduces an integrated framework which includes a ZigBee based sensor network and underlying multi-agent software (MAS) components. Several different types of sensors were integrated with the ZigBee host devices to produce compact multi-functional sensor units. The MAS framework incorporates the belief-desire-intention (BDI) abstraction with ontology support (provided via explicit knowledge bases). The different software agent types have been developed to work with sensor hardware to conduct resource negotiation, to optimize battery utilization, to monitor building space in a non-intrusive way and to reason about its usage through real time ontology model queries. The deployed sensor network shows promising intelligent characteristics, and it has been applied in several on-going research projects as an underlying decision making service. More applications and larger deployments have been planned for future work.
The development and maintenance of domain-specific application on- tologies require knowledge input from domain experts who are usually without any formal ontology or AI background. When dealing with large-scale ontologies, for example of the kind with which we are currently familiar in the biomedical spheres, quality assurance becomes important in minimizing modelling mistakes and the ap- plication errors which they bring in their wake. In this paper we describe how the upper-level framework BFO (for: Basic Formal Ontology), developed by the Insti- tute for Formal Ontology and Medical Information Science, is being used to provide automatic error detection and run-time modelling support to the development of LinKBase®, a large-scale medical domain ontology developed by Language and Computing NV to serve a range of natural language processing applications.
The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources - for example pertaining to genes and proteins, drugs and diseases - secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. Unfortunately, however, these efforts are hampered by a constellation of social, psychological legal and other forces, whose countervailing effects are magnified by constant increases in available data and computing power. Patients, hospitals and governments are reluctant to share data; physicians are reluctant to use computerized forms in preparing patient reports; nurses, physicians and medical researchers in different specialities each insist on using their own terminologies, addressing needs which are rarely consistent with the needs of information integration.
Ontology engineering is one of the basic components of Semantic Web technology, Ontology engineering provides semantic clarity,
explicitness, and facilitates the reusability of represented information and knowledge. We explain the major components of
typical ontologies, and the principles behind and different approaches to ontology design. We also discuss the common problems
encountered by ontology developers. As a demonstrative example we analyze the MGED (Microarray Gene Expression Data) ontology
for describing microarray experiments. The MGED Ontology (MO) is a pioneering attempt to formalize the description of microarray
experiments in biology. It has had a significant practical impact on the organization and execution of microarray experiments,
as well as on the storage and sharing of microarray experiment results. However, analysis of MO reveals design problems that
are common for other ontologies in biology. A generic ontology of experiments as a possible solution is discussed.
Ontologies are commonly used in computer science either as a reference model to support semantic interoperability, or as an
artifact that should be efficiently represented to support tractable automated reasoning. This duality poses a tradeoff between
expressivity and computational tractability that should be addressed in different phases of an ontology engineering process.
The inadequate choice of a modeling language, disregarding the goal of each ontology engineering phase, can lead to serious
problems in the deployment of the resulting model. This article discusses these issues by making use of an industrial case
study in the domain of Oil and Gas. We make explicit the differences between two different representations in this domain,
and highlight a number of concepts and ideas that were implicit in an original OWL-DL model and that became explicit by applying
the methodological directives underlying an ontologically well-founded modeling language.
To improve the performance of building facility management tools and optimize operational costs, a semantic model is being developed that is synchronized in almost real time with a range of sensors throughout the building. The semantic aspect of the model will be comprised of novel ontological perspectives with identified scopes and restricted domain theories that will simplify the modeling representations to deliver easier knowledge maintenance and continued integrity of the overall system. Specialized ontologies are linked to shared higher level abstract ontologies (to facilitate interoperation), and target a wide range of domains including those to capture physical processes and product models.
In philosophy, the term ontology has been used sin ce the 17 th century to refer both to a philosophical discipline (Ontology with a capital " O"), and as a domain-independent system of categori es that can be used in the conceptualization of domain -specific scientific theories. In the past decades there has been a growing interest in the subject of ontology in computer and information sciences. In the last f ew years, this interest has expanded considerably in t he context of the Semantic Web and MDA (Model-Driven Architecture) research efforts, and due to the role ontologies are perceived to play in these initiati ves. In this paper, we explore the relations between Ontology an d ontologies in the philosophical sense with domain ontologies in computer science. Moreover, we elaborate on formal characterizations for the notions of ontology, conceptualization and metamodel, as well as on the relations between these notions. Addition ally, we discuss a set of criteria that a modeling langua ge should meet in order to be considered a suitable language to model phenomena in a given domain, and present a systematic framework for language evaluation and design. Furthermore, we argue for th e importance of ontology in both philosophical sens es aforementioned for designing and evaluating a suita ble general ontology representation language, and w e address the question whether the so-called Ontology Web languages can be considered as suitable genera l ontology representation languages. Finally, we moti vate the need for two complementary classes of modeling languages in Ontology Engineering addressing two separate sets of concerns.
Organizations define strategies and establish business goals aiming to be competitive. The process performance analysis supports goals monitoring, allowing to detect and to treat threats to goals achievement. In this context, measurement is essential. The collected data for measures are used to analyze the process performance and to guide informed decisions that lead to the achievement of business and technical goals. For software organizations, the process performance analysis is a high maturity practice. In this context, although there are several standards that address the importance of software measurement and its use in process performance analysis, the vocabulary used by these standards concerning software measurement is diverse. In order to establish a conceptualization regarding this domain, we developed a Software Measurement Ontology (SMO), grounded in the Unified Foundational Ontology. In this paper, we present a fragment of SMO with focus on software process behavior analysis.
Ontology is a significant research theme in GIScience. While some researchers believe that the progress in GIScience is being directed through an engagement with the concept of ontology, some dismiss it as irrelevant. This paper is aimed at (i) exploring the theoretical and practical roles of ontologies; (ii) making the definitions and terminology explicit; (iii) assessing the applicability of ontology to problems in the geographical domain; and (iv) assessing whether a unified approach to ontology exists in GIScience. The results will be helpful for GIScientists in (i) understanding the validity of employing ontology within their own work, (ii) assessing what operational framework of terms and methods to use for developing their own ontology, and (iii) to assess what existing ontological models are available and applicable within their domain or application. A comprehensive and critical review will also help in identifying the signficant issues and directing future research agenda in GIScience.
This paper presents a formalized ontological framework for the analysis of multiscale classifications of geographic objects.
We propose a set of logical principles that guide such geographic classifications. These principles are represented as definitions
and axioms of the first-order predicate logic. Then we demonstrate an application of these principles with a practical example
of the “National Hierarchical Framework of Ecological Units.” The study presents a minimal set of entities and relation need
for such formalizations and emphasizes the need to distinguish clearly between classes of ecosystems and ecosystems-individuals
physically located on the Earth surface. The ontological framework proposed in the paper has the potential to be used to facilitate
interoperability between such geographic classifications.
To automatically deliver enhanced knowledge relating to building use, for tasks such as facility management (FM), a software system has been developed that exploits the combination of a number of technologies. As well as generating useful knowledge for decision support, the software aims to remove reliance on expert users, be self configuring, continually adapt to the environment, and employ learning to evolve its performance. The system is realised centrally by a multi agent society in which the agents are characterised by the strong notion of agency using the BDI (belief, desire, intention) model. In most existing applications in construction agents are task focussed rather than the goal focussed deliberative agents employed here. The BDI model is a ‘natural’ (human) abstraction for modelling complex systems, and goals are a stable way to define required behaviour. The agents are supported by a range of ontologies describing the semantics of the domain as well as aspects of agents’ goals. Furthermore the agents utilise a distributed network of readily available wired and wireless sensors and associated data storage providing access to near real time and historical data, as well as an Industry Foundation Classes (IFC) model describing building geometry and construction. The system produced can be used by non-specialist users, simply requiring an IFC specification of the building and sensor locations. Agents infer the roles of the sensors from an ontology together with context, and assign appropriate roles. The agents individually and cooperatively work towards identifying the usage and dynamics of arbitrarily sized spaces in buildings. Such knowledge can be used to support FM decisions such as the optimisation of the energy consumption/environmental comfort demand trade-off. Negotiation is used to increase robustness as well as to fill in missing information. The limitations of practical application of the technologies that failed to deliver expected benefit are also detailed.
In this thesis, we aim at contributing to the theory of conceptual modeling and ontology representation. Our main objective here is to provide ontological foundations for the most fundamental concepts in conceptual modeling. These foundations comprise a number of ontological theories, which are built on established work on philosophical ontology, cognitive psychology, philosophy of language and linguistics. Together these theories amount to a system of categories and formal relations known as a foundational ontology
Biomedical ontologies are typically structured in a biaxial way, reflecting both a taxonomic (is-a) and a partonomic (part-of) hierarchy. Commonly used biomedical terminologies, which incorporate such distinctions excel in terms of broad coverage but lack a rigid formal foundation. The latter, however, is a prerequisite for automated reasoning. For the biomedical domain, it is not only crucial to cope with ontological dependencies between wholes and their parts but also with specific reasoning patterns which underlie the propagation of roles across partonomic hierarchies.
We scale down part-whole reasoning to subsumption-based taxonomic reasoning within the formal framework of a parsimonious variant of description logics (viz. ALC).
We provide a formal basis for ontological engineering in the domain of biomedicine, as far as part-whole relationships are concerned, by addressing typical reasoning patterns encountered in this domain.
Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes and diseases as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language.
We describe the ontology engineering processes and their supporting technologies at L&C, a company developing intelligent
medical applications based on ontologies. We describe the principal tasks that the modellers of our ontology have to execute,
how they are supported and guided by some specifically ontology-focused management practices, and how (semi-)automated technology
can also aid in their support and guidance, so as to produce a higher quality and quantity of ontology product. The ontology
processes include the development of new structures of concepts and relations, the integration of other ontologies and terminologies,
the integration of the ontology to natural language applications, and the reforming of the current ontology’s formal structure.
The automated supports we talk about include OntoClean, a principled methodology for analyzing ontological properties and
their constraints. We finally note how far we think our ontology technology comes to some proposed desiderata recently given
for “enterprise standard” ontology environments.
SNAP and SPAN: Towards dynamic special ontology Ontology Mapping: The State of the Art
- P Grenon
- B Smith
Grenon P, Smith B. SNAP and SPAN: Towards
dynamic special ontology. Forthcoming.
Kalfoglou, Y, Schorlemmer, M. Ontology Mapping:
The State of the Art. The Knowledge Engineering
Review 18(1), 2003.
A Theory of Granular Partitions. Foundations of Geographic Information Science
- T Bittner
- Smith
Bittner, T, Smith, B. A Theory of Granular Partitions.
Foundations of Geographic Information Science,
Duckham, M, Goodchild, M, and Worboys, M, eds.,
London: Taylor & Francis Books, 2003: 117-151.
The Ontology of the Gene Ontology Proceedings of the AMIA Symposium 2003, forthcoming. Smith B. Mereotopology: a theory of parts and boundaries
- B Smith
- J Williams
- S Schulze-Kremer
Smith B, Williams J, Schulze-Kremer S. The Ontology
of the Gene Ontology. Proceedings of the AMIA
Symposium 2003, forthcoming.
Smith B. Mereotopology: a theory of parts and
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