Showing papers on "Ontology-based data integration published in 2000"

Algorithm and Tool for Automated Ontology Merging and Alignment

Abstract: Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide semantics for annotations in Web pages. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. The processes of ontology alignment and merging are usually handled manually and often constitute a large and tedious portion of the sharing process. We have developed and implemented PROMPT, an algorithm that provides a semi-automatic approach to ontology merging and alignment. PROMPT performs some tasks automatically and guides the user in performing other tasks for which his intervention is required. PROMPT also determines possible inconsistencies in the state of the ontology, which result from the user’s actions, and suggests ways to remedy these inconsistencies. PROMPT is based on an extremely general knowledge model and therefore can be applied across various platforms. Our formative evaluation showed that a human expert followed 90% of the suggestions that PROMPT generated and that 74% of the total knowledge-base operations invoked by the user were suggested by PROMPT.

PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment

Abstract: Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide semantics for annotations in Web pages. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. The processes of ontology alignment and merging are usually handled manually and often constitute a large and tedious portion of the sharing process. We have developed and implemented PROMPT, an algorithm that provides a semi-automatic approach to ontology merging and alignment. PROMPT performs some tasks automatically and guides the user in performing other tasks for which his intervention is required. PROMPT also determines possible inconsistencies in the state of the ontology, which result from the user’s actions, and suggests ways to remedy these inconsistencies. PROMPT is based on an extremely general knowledge model and therefore can be applied across various platforms. Our formative evaluation showed that a human expert followed 90% of the suggestions that PROMPT generated and that 74% of the total knowledge-base operations invoked by the user were suggested by PROMPT.

Ontology-based knowledge representation for bioinformatics

Abstract: Much of biology works by applying prior knowledge ('what is known') to an unknown entity, rather than the application of a set of axioms that will elicit knowledge. In addition, the complex biological data stored in bioinformatics databases often require the addition of knowledge to specify and constrain the values held in that database. One way of capturing knowledge within bioinformatics applications and databases is the use of ontologies. An ontology is the concrete form of a conceptualisation of a community's knowledge of a domain. This paper aims to introduce the reader to the use of ontologies within bioinformatics. A description of the type of knowledge held in an ontology will be given.The paper will be illustrated throughout with examples taken from bioinformatics and molecular biology, and a survey of current biological ontologies will be presented. From this it will be seen that the use to which the ontology is put largely determines the content of the ontology. Finally, the paper will describe the process of building an ontology, introducing the reader to the techniques and methods currently in use and the open research questions in ontology development.

Dynamic Ontologies on the Web

Abstract: We discuss the problems associated with managing ontologies in distributed environments such as the Web. The Web poses unique problems for the use of ontologies because of the rapid evolution and autonomy of web sites. We present SHOE, a web-based knowledge representation language that supports multiple versions of ontologies. We describe SHOE in the terms of a logic that separates data from ontologies and allows ontologies to provide different perspectives on the data. We then discuss the features of SHOE that address ontology versioning, the effects of ontology revision on SHOE web pages, and methods for implementing ontology integration using SHOE’s extension and version mechanisms.

An ontology for biological function based on molecular interactions

Abstract: Motivations: A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function. Results: The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics. The functional ontology developed for the EcoCyc database is presented. This ontology can encode a diverse array of biochemical processes, including enzymatic reactions involving smallmolecule substrates and macromolecular substrates, signal-transduction processes, transport events, and mechanisms of regulation of gene expression. The ontology is validated through its use to express complex functional queries for the EcoCyc DB.

A Roadmap to Ontology Specification Languages

Abstract: The interchange of ontologies across the World Wide Web (WWW) and the cooperation among heterogeneous agents placed on it is the main reason for the development of a new set of ontology specification languages, based on new web standards such as XML or RDF. These languages (SHOE, XOL, RDF, OIL, etc) aim to represent the knowledge contained in an ontology in a simple and human-readable way, as well as allow for the interchange of ontologies across the web. In this paper, we establish a common framework to compare the expressiveness and reasoning capabilities of "traditional" ontology languages (Ontolingua, OKBC, OCML, FLogic, LOOM) and "web-based" ontology languages, and conclude with the results of applying this framework to the selected languages.

Ontology Engineering beyond the Modeling of Concepts and Relations

Abstract: This papers presents a new approach for modeling large-scale ontologies. We extend well-established methods for modeling concepts and relations by transportable methods for modeling ontological axioms. The gist of our approach lies in the way we treat the majority of axioms. They are categorized into different types and specified as complex objects that refer to concepts and relations. Considering language and system particularities, this first layer of representation is then translated into the target representation language. This two-layer approach benefits engineering, because the intended meaning of axioms is captured by the categorization of axioms. Classified object representations allow for versatile access to and manipulations of axioms via graphical user interfaces.

Ontology for database design and application development

Abstract: A system and method lets a user create or import ontologies and create databases and related application software. These databases can be specially tuned to suit a particular need, and each comes with the same error-detection rules to keep the data clean. Such databases may be searched based on meaning, rather than on words-that-begin-with-something. And multiple databases, if generated from the same basic ontology can communicate with each other without any additional effort. Ontology management and generation tools enable enterprises to create databases that use ontologies to improve data integration, maintainability, quality, and flexibility. Only the relevant aspects of the ontology are targeted, extracting out a sub-model that has the power of the full ontology restricted to objects of interest for the application domain. To increase performance and add desired database characteristics, this sub-model is translated into a database system. Java-based object-oriented and relational application program interfaces (APIs) are then generated from this translation, providing application developers with an API that exactly reflects the entity types and relations (classes and methods) that are represented by the database. This generation approach essentially turns the ontology into a set of integrated and efficient databases.

The TEXT-TO-ONTO Ontology Learning Environment

Abstract: Ontologies have become an important means for structuring information and information systems and, hence, important in knowledge as well as in software engineering. However, there remains the problem of engineering large and adequate ontologies within short time frames in order to keep costs low. For this purpose, we present the TEXT-TO-ONTO Ontology Learning Environment, which is based on a general architecture for discovering conceptual structures and engineering ontologies from text. Our Ontology Learning Environment supports as well the acquisition of conceptual structures as mapping linguistic resources to the acquired structures.

Towards a methodology for ontology based model engineering

Abstract: The philosophical discipline of Ontology is evolving towards an engineering discipline, and in this evolution the need for a principled methodology has clearly arisen. In this paper, we briefly discuss our recent work towards developing a methodology for ontology-based model engineering. This methodology builds on previous methodology efforts, and is founded on important analytic notions that have been drawn from Philosophy and adapted to Engineering: identity, unity, rigidity, and dependence. We demonstrate how these techniques can be used to analyze properties, which clarifies many misconceptions about taxonomies and helps bring substantial order to ontologies.

Ontology Learning from Text

Abstract: Ontologies have shown their usefulness in application areas such as information integration, natural language processing, metadata for the world wide, to name but a few However, there remains the problem of engineering large and adequate ontologies within short time frames in order to keep costs low We here present a general architecture for discovering conceptual structures and engineering ontologies from text and a new approach for discovering non-taxonomic conceptual relations from text

Knowledge-based integration of neuroscience data sources

Abstract: The need for information integration is paramount in many biological disciplines, because of the large heterogeneity in both the types of data involved and in the diversity of approaches (physiological, anatomical, biochemical, etc.) taken by biologists to study the same or correlated phenomena. However, the very heterogeneity makes the task of information integration very difficult since two approaches studying different aspects of the same phenomena may not even share common attributes in their schema description. The paper develops a wrapper-mediator architecture which extends the conventional data- and view-oriented information mediation approach by incorporating additional knowledge modules that bridge the gap between the heterogeneous data sources. The semantic integration of the disparate local data sources employs F-logic as a data and knowledge representation and reasoning formalism. We show that the rich object oriented modeling features of F-logic together with its declarative rule language and the uniform treatment of data and metadata (schema information) make it an ideal candidate for complex integration tasks. We substantiate this claim by elaborating on our integration architecture and illustrating the approach using real world examples from the neuroscience domain. The complete integration framework is currently under development; a first prototype establishing the viability of the approach is operational.

Construction and Deployment of a Plant Ontology

Abstract: Although the necessity of an ontology and ontological engineering is well-understood, there has been few success stories about ontology construction and its deployment to date. This paper presents an activity of ontology construction and its deployment in an interface system for an oil-refinery plant operation which has been done under the umbrella of Human-Media Project for four years. It also describes the reasons why we need an ontology, what ontology we built, what environment we used for building the ontology and how the ontology is used in the system. The interface has been developed intended to establish a sophisticated technology for advanced interface for plant operators and consists of several agents. The system has been implemented and preliminary evaluation has been done successfully.

Evaluating Knowledge Representation and Reasoning Capabilites of Ontology Specification Languages

Abstract: The interchange of ontologies across the World Wide Web (WWW) and the cooperation among heterogeneous agents placed on it is the main reason for the development of a new set of ontology specification languages, based on new web standards such as XML or RDF These languages (SHOE, XOL, RDF, OIL, etc) aim to represent the knowledge contained in an ontology in a simple and human-readable way, as well as allow for the interchange of ontologies across the web In this paper, we establish a common framework to compare the expressiveness of "traditional" ontology languages (Ontolingua, OKBC, OCML, FLogic, LOOM) and "web-based" ontology languages As a result of this study, we conclude that different needs in KR and reasoning may exist in the building of an ontology-based application, and these needs must be evaluated in order to choose the most suitable ontology language(s)

Extracting a domain-specific ontology from a corporate intranet

Abstract: This paper describes our actual and ongoing work in supporting semi-automatic ontology acquisition from a corporate intranet of an insurance company. A comprehensive architecture and a system for semi-automatic ontology acquisition supports processing semi-structured information (e.g. contained in dictionaries) and natural language documents and including existing core ontologies (e.g. GermaNet, WordNet). We present a method for acquiring a application-tailored domain ontology from given heterogeneous intranet sources.

Domain Ontology Management Environment

Abstract: Service-oriented business-to-business e-commerce requires dynamic and open interoperable information systems. Although most large organisations have information regarding products, services and customers stored in databases, and XML/DTD allows these to be published over the Internet, sharing information among these systems has been prevented by semantic heterogeneity. True electronic commerce will not happen until the semantics of the terms used to model these information systems can be captured and processed by computers. Developing a machine processable ontology (vocabulary) is intrinsically hard. The semantics of a term varies from one context to another. We believe ontology engineering will be a major effort of any future application development. In this paper we describe our work on building a Domain Ontology Management Environment (DOME). DOME is developing techniques for ontology-based information content description and a suite of tools for domain ontology management. Information content description extends traditional meta data to an ontology. This makes it possible to dynamically find relevant data sources based on content and to integrate them as needed.

An Evaluation of Ontology Exchange Languages for Bioinformatics

Abstract: Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they satisfied each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusion of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua.

Ontology Engineering for Distributed Collaboration in Manufacturing

Abstract: The problems of inter-operability are acute for manufacturing applications, as applications using process specifications do not necessarily share syntax and definitions of concepts. The Process Specification Language developed at the National Institute of Standards and Technology proposes a formal ontology and translation mechanisms representing manufacturing concepts. When an application becomes ‘PSL compliant,’ its concepts are expressed using PSL, with a direct one-to-one mapping or with a mapping under certain conditions. An example of how to resolve semantic ambiguities is provided for the manufacturing concept ‘resource’. Finally some ideas on how to use PSL for inter-operability in agent-based systems are presented.

Knowledge based information integration systems

Abstract: Information integration systems provide facilities that support access to heterogeneous information sources in a way that isolates users from differences in the formats, locations and facilities of those sources. A number of systems have been proposed that exploit knowledge based techniques to assist with information integration, but it is not always obvious how proposals differ from each other in their scope, in the quality of integration afforded, or in the cost of exploitation. This paper presents a framework for the comparison of proposals for information integration systems, and applies the framework to a range of representative proposals. It is shown that proposals differ greatly in all of the criteria stated and that the selection of an approach is thus highly dependent on the requirements of specific applications.

Reference Ontology and (ONTO)2 Agent: The Ontology Yellow Pages

Abstract: Knowledge reuse by means of ontologies faces three important problems at present: (1) there are no standardized identifying features that characterize ontologies from the user point of view; (2) there are no web sites using the same logical organization, presenting relevant information about ontologies; and (3) the search for appropriate ontologies is hard, time-consuming and usually fruitless. To solve the above problems, we present: (1) a living set of features that allow us to characterize ontologies from the user point of view and have the same logical organization; (2) a living domain ontology about ontologies (called Reference Ontology) that gathers, describes and has links to existing ontologies; and (3) (ONTO)2 Agent, the ontology-based WWW broker about ontologies that uses Reference Ontology as a source of its knowledge and retrieves descriptions of ontologies that satisfy a given set of constraints.

A cooperative tool for facilitating knowledge management

Abstract: Nowadays, we can find systems and environments supporting processes of ontology building. However, these processes have not been specified enough yet. In this work, a real environment for integrating ontologies supplied by a predetermined set of (experts) users, who might be distributed through a communication network and working cooperatively in the integration process, is introduced. In this environment, the (expert) user can check for the ontology that is being produced, so he/she is able to refine his/her private ontology. Furthermore, the experts who take part of the ontology construction process are allowed to use their own terminology even for requesting information about the global-derived ontology until a specific instant after the integration.

Consistent Integration of Formal Methods

Abstract: The usability of formal concepts for system design depends essentially on their integration in the design process. We discuss several possible levels of integration: technical integration of tools considering APIs and tool interfaces, conceptual integration of metamodels of description formalisms combined with hard and soft constraints, semantical integration of semantics of description techniques using a common semantic model, and finally methodical integration by an embedding in the development process. We show the feasibility of such an integrated approach and its advantages presenting AutoFocus/Quest, a formal method CASE-Tool with its levels of integration. Parts of a banking system model are used as example.

Ontology's Crossed Life Cycles

Abstract: This paper presents the idea that the life cycle of an ontology is highly impacted as a result of the process of reusing it for building another ontology. One of the more important results of the experiment presented is how the different activities to be carried out during the development of a specific ontology may involve performing other types of activities on other ontologies already built or under construction. We identify in that paper new intra-dependencies between activities carried out inside the same otology and interdependencies between activities carried out in different ontologies. The interrelation between life cycles of several ontologies provokes that integration has to be approached globally rather than as a mere integration of out implementation.

A note on the refinement of ontologies

Abstract: Ontologies have emerged as one of the key issues in information integration and interoperability and in their application to knowledge management and electronic commerce. A trend towards formal methods for ontology management is obvious. This paper discusses a concept which can be expected to be of great importance to formal ontology management, and which is well-known in traditional software development: refinement. We define and discuss ontology refinement, give illustrating examples, and highlight its advantages as compared to other forms of ontology revision. © 2000 John Wiley & Sons, Inc.

Taxonomy of Factors for Information System Application Integration

Abstract: Application integration technology is a new class of system integration that involves the development of new strategic business solutions. These securely integrate functionality from disparate applications. In considering this, the presented paper seeks to describe the application integration arena and proposes a novel taxonomy for this new scope of technology. Furthermore, it analyses factors that are related with the impact of application integration on companies and presents a number of research questions that are associated with this area.

The TheaterLoc Virtual Application

Abstract: Although much has been written about various information integration technologies, little has been said regarding how to combine these technologies together to build an entire “virtual” application. In this paper, we describe the design and implementation of TheaterLoc, an information integration application that allows users to retrieve information about theaters and restaurants for a variety of cities in the United States, including an interactive map depicting their relative locations and video trailers of the movies playing at the selected theaters. The data retrieved by TheaterLoc comes from five distinct heterogeneous and distributed sources. The enabling technology used to achieve the integration includes the Ariadne information mediator and wrappers for each of the web-based data sources. We focus in detail on the mediator technologies, such as data modeling, source axiom compilation, and query planning. We also describe how the wrappers present an interface for querying data on web sites, aiding in information retrieval used during data integration. Finally, we discuss some of the major integration challenges we encountered and our plans to address them.