Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases (ICD) as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the ICD, which is currently under active development by the WHO contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding how these stakeholders collaborate will enable us to improve editing environments that support such collaborations. We uncover how large ontology-engineering projects, such as the ICD in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users subsequently change) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain.Comment: Published in the Journal of Biomedical Informatic

A Shared Ontology Approach to Semantic Representation of BIM Data

Architecture, engineering, construction and facility management (AEC-FM) projects involve a large number of participants that must exchange information and combine their knowledge for successful completion of a project. Currently, most of the AEC-FM domains store their information about a project in text documents or use XML, relational, or object-oriented formats that make information integration difficult. The AEC-FM industry is not taking advantage of the full potential of the Semantic Web for streamlining sharing, connecting, and combining information from different domains. The Semantic Web is designed to solve the information integration problem by creating a web of structured and connected data that can be processed by machines. It allows combining information from different sources with different underlying schemas distributed over the Internet. In the Semantic Web, all data instances and data schema are stored in a graph data store, which makes it easy to merge data from different sources. This paper presents a shared ontology approach to semantic representation of building information. The semantic representation of building information facilitates finding and integrating building information distributed in several knowledge bases. A case study demonstrates the development of a semantic based building design knowledge base

OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories

In collaborative agile ontology development projects support for modular reuse of ontologies from large existing remote repositories, ontology project life cycle management, and transitive dependency management are important needs. The Apache Maven approach has proven its success in distributed collaborative Software Engineering by its widespread adoption. The contribution of this paper is a new design artifact called OntoMaven. OntoMaven adopts the Maven-based development methodology and adapts its concepts to knowledge engineering for Maven-based ontology development and management of ontology artifacts in distributed ontology repositories.Comment: Pre-print submission to 9th International Workshop on Semantic Web Enabled Software Engineering (SWESE2013). Berlin, Germany, December 2-5, 201

An Overview of the BFO - Basic Formal Ontology - and Its Applicability for Satellite Systems

This work aims to present an overview of the top-level ontology BFO - Basic Formal Ontology - and its applicability for Satellite Systems. As an upper level ontology, the BFO was designed to be extended, providing the basis for the specification of detailed representational artifacts about scientific information domains. These aspects and the challenges of satellite systems complexity and large size compose a suitable scenario for the creation of a specialized dialect to improve efficiency and accuracy when modeling such systems. By analyzing BFO based ontologies in other disciplines and existing satellite models it is possible to describe an application for satellite systems, which can provide a foundation for the creation of a concrete ontology to be applied on satellite modeling

Ontology engineering for simulation component reuse

Commercial-off-the-shelf (COTS) simulation packages (CSPs) are widely used in industry, although they have yet to operate across organizational boundaries. Reuse across organizations is restricted by the same semantic issues that restrict the inter-organizational use of web services. The current representations of web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging semantic web. Semantic models, in the form of ontology, utilized by web service discovery and deployment architectures provide one approach to support simulation model reuse. Semantic interoperation is achieved through the use of simulation component ontologies to identify required components at varying levels of granularity (including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The paper presents the development of an ontology, connector software and web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organizational simulation, adopting a less intrusive interface between participants. Although specific to CSPs the work has wider implications for the simulation community

Using Ontologies for the Design of Data Warehouses

Obtaining an implementation of a data warehouse is a complex task that forces designers to acquire wide knowledge of the domain, thus requiring a high level of expertise and becoming it a prone-to-fail task. Based on our experience, we have detected a set of situations we have faced up with in real-world projects in which we believe that the use of ontologies will improve several aspects of the design of data warehouses. The aim of this article is to describe several shortcomings of current data warehouse design approaches and discuss the benefit of using ontologies to overcome them. This work is a starting point for discussing the convenience of using ontologies in data warehouse design.Comment: 15 pages, 2 figure

Drawing OWL 2 ontologies with Eddy the editor

In this paper we introduce Eddy, a new open-source tool for the graphical editing of OWL~2 ontologies. Eddy is specifically designed for creating ontologies in Graphol, a completely visual ontology language that is equivalent to OWL~2. Thus, in Eddy ontologies are easily drawn as diagrams, rather than written as sets of formulas, as commonly happens in popular ontology design and engineering environments. This makes Eddy particularly suited for usage by people who are more familiar with diagramatic languages for conceptual modeling rather than with typical ontology formalisms, as is often required in non-academic and industrial contexts. Eddy provides intuitive functionalities for specifying Graphol diagrams, guarantees their syntactic correctness, and allows for exporting them in standard OWL 2 syntax. A user evaluation study we conducted shows that Eddy is perceived as an easy and intuitive tool for ontology specification

A framework for deriving semantic web services

Web service-based development represents an emerging approach for the development of distributed information systems. Web services have been mainly applied by software practitioners as a means to modularize system functionality that can be offered across a network (e.g., intranet and/or the Internet). Although web services have been predominantly developed as a technical solution for integrating software systems, there is a more business-oriented aspect that developers and enterprises need to deal with in order to benefit from the full potential of web services in an electronic market. This ‘ignored’ aspect is the representation of the semantics underlying the services themselves as well as the ‘things’ that the services manage. Currently languages like the Web Services Description Language (WSDL) provide the syntactic means to describe web services, but lack in providing a semantic underpinning. In order to harvest all the benefits of web services technology, a framework has been developed for deriving business semantics from syntactic descriptions of web services. The benefits of such a framework are two-fold. Firstly, the framework provides a way to gradually construct domain ontologies from previously defined technical services. Secondly, the framework enables the migration of syntactically defined web services toward semantic web services. The study follows a design research approach which (1) identifies the problem area and its relevance from an industrial case study and previous research, (2) develops the framework as a design artifact and (3) evaluates the application of the framework through a relevant scenario