WebProt\'eg\'e: A Cloud-Based Ontology Editor

We present WebProt\'eg\'e, a tool to develop ontologies represented in the Web Ontology Language (OWL). WebProt\'eg\'e is a cloud-based application that allows users to collaboratively edit OWL ontologies, and it is available for use at https://webprotege.stanford.edu. WebProt\'ege\'e currently hosts more than 68,000 OWL ontology projects and has over 50,000 user accounts. In this paper, we detail the main new features of the latest version of WebProt\'eg\'e

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 Requirement Ontology To Guide The Analysis Of System Life Cycle Processes

Economies prosper by designing, manufacturing, and servicing a variety of innovative products, for example airplanes, healthcare services, infrastructure development, and information technologies. Having the right competency (aka information processing skills) for designing, manufacturing, and servicing these products is necessary for economies to exploit new opportunities. These products have become more complex to design, manufacture and serve involving people with different education, language, and possibly globally distributed. In order to create these products, information processing skills have been put to the limits causing competitiveness problems. Detailed analysis has associated these problems to requirements. Requirements involve to process different kinds of information (e.g., texts, presentations, sketches, graphs, tables, drawings, engineering analysis, and managerial analysis) during system life cycle processes (i.e., from idea generation to retirement of a product); where at each stage, information has different content (e.g., aspect, medium, and format). Therefore, a root cause associated to requirements can be attributed to a lack of a common vocabulary to communicate this variety of information in the context of system life cycle processes. Theories and models have been employed as solution to solve this communication problem; however, current practice results suggest that a more effective solution is needed. As a result, this thesis employs an ontology as a means to solve the problem which is also an alternative and complement to theories and models. In general, a requirement ontology for system life cycle processes defines the core concepts and their relationships which combined define a common vocabulary in the context of requirements for system life cycle processes. A common vocabulary enables better communication and understanding among people as a core tool to support information processing skills. Hence, an ontology as a common vocabulary is the foundation to increase competitiveness to design, manufacture, and serve a variety of innovative products; which may lead to economies prosperity. More specifically, this thesis proposes a requirement ontology for system life cycle processes as a tool to be used to guide the analysis of these processes. Based on the fact that the ontology refers to the knowledge domain of design, guidance from a design theory (i.e., Environment-Based Design) was adopted to create the proposed ontology. Four related ontologies were created based on frequency analysis in this thesis, but the proposed core ontology contains a vocabulary of 50+2 concepts and 24 types of relationships. The proposed core ontology has been validated from different perspectives: 1) design theory (i.e., Environment-Based Design) compliance, 2) creation and evaluation from international standards (ISO 15288:2015 and ISO 29148:2011) and three European research efforts, and 3) retrospection from three case studies: a) Total Quality Management System Guideline Development Using Environment-Based Design for Area Development Planning, b) Designing the Right Framework for Healthcare Decision Support, and c) Integrating learning through design methodologies in aircraft design. This type of validation enables to speculate that the ontology can be generalized to the scope of requirements for different engineering endeavours. At the current stage of research, the proposed ontology is an information technology product that contributes to the actual knowledge base two major aspects: 1) a common vocabulary in the context of requirements for system lifecycle processes, and 2) a replicable ontology design process that can be extended to other domains of knowledge. The current stage of the proposed ontology shall be moved forward as future research. Two major venues for future research can be considered. First, expose the proposed ontology to potential users to improve the current stage of development of the ontology. Second, use the ontology as a tool to guide the analysis of system life cycle processes (e.g., ilities or specialty engineering). The current stage of the proposed ontology and future research venues shall improve communication and understanding among people as a core tool to support information processing skills for designing, manufacturing, and servicing a variety of innovative products