How ontologies are made: Studying the hidden social dynamics behind collaborative ontology engineering projects

Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product. In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to their construction is critical not only in understanding but consequently also in evaluating the ontologies. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches.     

A software engineering approach to ontology building

Ontologies are the backbone of the Semantic Web, a semantic-aware version of the World Wide Web. The availability of large-scale high quality domain ontologies depends on effective and usable methodologies aimed at supporting the crucial process of ontology building. Ontology building exhibits a structural and logical complexity that is comparable to the production of software artefacts. This paper proposes an ontology building methodology that capitalizes the large experience drawn from a widely used standard in software engineering: the Unified Software Development Process or Unified Process (UP). In particular, we propose UP for ONtology (UPON) building, a methodology for ontology building derived from the UP. UPON is presented with the support of a practical example in the eBusiness domain. A comparative evaluation with other methodologies and the results of its adoption in the context of the Athena EU Integrated Project are also discussed.     

ANEMONE: An environment for modular ontology development

Many real-world ontologies contain thousands of terms and are developed by multiple participants. The use of monolithic ontologies can cause problems that affect various stages of the ontology life cycle. Thus, there is an urgent need for tools and methodologies that facilitate modular ontology design. The benefits of a modular approach include division of labor, scalability, partial reuse, and broadened participation. This article presents a methodology for modular ontology development. The main idea is to facilitate an interoperable hierarchical network of ontology modules. Modules are designed as a combination of more abstract modules in higher levels of the hierarchy. This methodology differs from previous methodologies in the way that it defines concrete development steps, to facilitate use by both naive and expert ontology developers. This methodology is also supported by ontology design patterns and a prototypical ontology development tool.     

Empirical findings on ontology metrics

Ontologies are becoming the preferred way of representing, dealing and reasoning with large volumes of information in several domains. In consequence, the creation, evaluation and maintenance of ontologies has become an engineering process that needs to be managed and measured using sound and reliable methods. As part of any ontology engineering or revision process, metrics can play a role helping in identifying possible problems or incorrect use of ontology elements, along with providing a kind of quality assessment that complements reviews requiring expert inspection. However, in spite of the fact that there are a number of ontology metric proposals described in the literature, there is a lack of empirical studies that provide a basis for their interpretation. This paper reports a systematic exploration of existing ontology metrics from a large set of ontologies extracted from the Swoogle search engine. The OntoRank value used inside the Swoogle to rank search results is used as a contrast for some existing metrics. The results show that the existing proposed metrics evaluated in general do not seem to be indicators of that ranking, but they can be helpful to identify particular kinds of ontologies.     

Efficient retrieval of ontology fragments using an interval labeling scheme

Nowadays very large domain ontologies are being developed in life-science areas like Biomedicine, Agronomy, Astronomy, etc. Users and applications can benefit enormously from these ontologies in very different tasks, such as visualization, vocabulary homogenizing and data classification. However, due to their large size, they are often unmanageable for these applications. Instead, it is necessary to provide small and useful fragments of these ontologies so that the same tasks can be performed as if the whole ontology is being used. In this work we present a novel method for efficiently indexing and generating ontology fragments according to the user requirements. Moreover, the generated fragments preserve relevant inferences that can be made with the selected symbols in the original ontology. Such a method relies on an interval labeling scheme that efficiently manages the transitive relationships present in the ontologies. Additionally, we provide an interval’s algebra to compute some logical operations over the ontology concepts. We have evaluated the proposed method over several well-known biomedical ontologies. Results show very good performance and scalability, demonstrating the applicability of the proposed method in real scenarios.     

BiOSS: A system for biomedical ontology selection

In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service.     

Semantic oriented ontology cohesion metrics for ontology-based systems

Ontologies play a core role to provide shared knowledge models to semantic-driven applications targeted by Semantic Web. Ontology metrics become an important area because they can help ontology engineers to assess ontology and better control project management and development of ontology based systems, and therefore reduce the risk of project failures. In this paper, we propose a set of ontology cohesion metrics which focuses on measuring (possibly inconsistent) ontologies in the context of dynamic and changing Web. They are: Number of Ontology Partitions (NOP), Number of Minimally Inconsistent Subsets (NMIS) and Average Value of Axiom Inconsistencies (AVAI). These ontology metrics are used to measure ontological semantics rather than ontological structure. They are theoretically validated for ensuring their theoretical soundness, and further empirically validated by a standard test set of debugging ontologies. The related algorithms to compute these ontology metrics also are discussed. These metrics proposed in this paper can be used as a very useful complementarity of existing ontology cohesion metrics.     

Terminological ontology learning and population using latent Dirichlet allocation

The success of Semantic Web will heavily rely on the availability of formal ontologies to structure machine understanding data. However, there is still a lack of general methodologies for ontology automatic learning and population, i.e. the generation of domain ontologies from various kinds of resources by applying natural language processing and machine learning techniques In this paper, the authors present an ontology learning and population system that combines both statistical and semantic methodologies. Several experiments have been carried out, demonstrating the effectiveness of the proposed approach.     

Using Bayesian decision for ontology mapping

Ontology mapping is the key point to reach interoperability over ontologies. In semantic web environment, ontologies are usually distributed and heterogeneous and thus it is necessary to find the mapping between them before processing across them. Many efforts have been conducted to automate the discovery of ontology mapping. However, some problems are still evident. In this paper, ontology mapping is formalized as a problem of decision making. In this way, discovery of optimal mapping is cast as finding the decision with minimal risk. An approach called Risk Minimization based Ontology Mapping (RiMOM) is proposed, which automates the process of discoveries on 1:1, n:1, 1:null and null:1 mappings. Based on the techniques of normalization and NLP, the problem of instance heterogeneity in ontology mapping is resolved to a certain extent. To deal with the problem of name conflict in mapping process, we use thesaurus and statistical technique. Experimental results indicate that the proposed method can significantly outperform the baseline methods, and also obtains improvement over the existing methods.     

Aondê: An ontology Web service for interoperability across biodiversity applications

Biodiversity research requires associating data about living beings and their habitats, constructing sophisticated models and correlating all kinds of information. Data handled are inherently heterogeneous, being provided by distinct (and distributed) research groups, which collect these data using different vocabularies, assumptions, methodologies and goals, and under varying spatio-temporal frames. Ontologies are being adopted as one of the means to alleviate these heterogeneity problems, thus helping cooperation among researchers. While ontology toolkits offer a wide range of operations, they are self-contained and cannot be accessed by external applications. Thus, the many proposals for adopting ontologies to enhance interoperability in application development are either based on the use of ontology servers or of ontology frameworks. The latter support many functions, but impose application recoding whenever ontologies change, whereas the first supports ontology evolution, but for a limited set of functions.This paper presents Aondê—a Web service geared towards the biodiversity domain that combines the advantages of frameworks and servers, supporting ontology sharing and management on the Web. By clearly separating storage concerns from semantic issues, the service provides independence between ontology evolution and the applications that need them. The service provides a wide range of basic operations to create, store, manage, analyze and integrate multiple ontologies. These operations can be repeatedly invoked by client applications to construct more complex manipulations. Aondê has been validated for real biodiversity case studies.     

A high-level electrical energy ontology with weighted attributes

One of the significant application areas of domain ontologies is known to be text analysis applications like information extraction and text classification systems, and semantic portals. In this paper, we present a high-level ontology for the electrical energy domain. This domain ontology has weighted attributes to cover the inherent fuzziness in the textual representations of its concepts. Additionally, we have included in the ontology the necessary attributes to align the ontology concepts to on-line collaborative knowledge bases like Wikipedia and linked open data sources like DBpedia, other attributes to facilitate its use in multilingual applications, and concepts to hold the named entities in the domain. The ultimate ontology is aligned with the previously proposed ontologies for the energy-related subdomains after extending the latter ones with weighted attributes. We make the ultimate form of the electrical energy ontology, as well as the extended versions of the domain ontologies for the subdomains, available for research purposes. Also included in the paper are sample text analysis applications which mainly exploit the weighted attributes within the ontology.     

OntoQualitas: A framework for ontology quality assessment in information interchanges between heterogeneous systems

Nowadays, Internet technologies and standards are being systematically used by enterprises as tools to provide an infrastructure to connect people, enterprises, and applications they are using. In such complex networked enterprises, it is increasingly challenging to interchange, share, and manage internal and external digital information. In this context, to achieve interoperability between information systems is a challenging task. In order to solve the interoperability problem at semantic level, several ontology-based approaches have emerged. Although methodologies, methods, techniques, and tools to support the ontology building process were proposed, there are no mature models to measure this process, and the quality of implemented ontologies remains a major concern. This paper presents a framework, OntoQualitas, for evaluating the quality of an ontology whose purpose is the information interchange between different contexts. OntoQualitas includes previous and new measures to evaluate the ontology considering its specific purpose. Additionally, an empirical validation of OntoQualitas is presented.     

Supply chain ontology: Review, analysis and synthesis

In an environment where supply chains compete against supply chains, information sharing among supply chain partners using information systems is a competitive tool. Supply chain ontology has been proposed as an important medium for attaining information systems interoperability. Ontology has its origin in philosophy, and the computing community has adopted ontology in its language. This paper presents a study of state of the art research in supply chain ontology and identifies the outstanding research gaps. Six supply chain ontology models were identified from a systematic review of literature. A seven point comparison framework was developed to consider the underlying concepts as well as application of the ontology models. The comparison results were then synthesised into nine gaps to inform future supply chain ontology research. This work is a rigorous and systematic attempt to identify and synthesise the research in supply chain ontology.     

Towards a Machine of a Process (MOP) ontology to facilitate e-commerce of industrial machinery

Adapting to user's requirements is a key factor for enterprise success. Despite the existence of several approaches that point in this direction, simplifying integration and interoperability among users, suppliers and the enterprise during product lifecycle, is still an open issue. Ontologies have been used in some manufacturing applications and they promise to be a valid approach to model manufacturing resources of enterprises (e.g. machinery and raw material). Nevertheless, in this domain, most of the ontologies have been developed following methodologies based on development from scratch, thus ontologies previously developed have been discarded. Such ontological methodologies tend to hold the interoperability issues in some level. In this paper, a method that integrates ontology reuse with ontology validation and learning is presented. An upper (top-level) ontology for manufacturing was used as a reference to evaluate and to improve specific domain ontology. The evaluation procedure was based on the systemic methodology for ontology learning (SMOL). As a result of the application of SMOL, an ontology entitled Machine of a Process (MOP) was developed. The terminology included in MOP was validated by means of a text mining procedure called Term Frequency–Inverse Document Frequency (TF–IDF) which was carried out on documents from the domain in this study. Competency questions were performed on preexisting domain ontologies and MOP, proving that this new ontology has a performance better than the domain ontologies used as seed.     

Investigating ontology development for engineering design support

Ontologies are now in widespread use as a means of formalizing domain knowledge in a way that makes it accessible, shareable and reusable. Nevertheless, to many, the nature and use of ontologies are unfamiliar. This paper takes a practical approach - through the use of example - to clarifying what ontologies are and how they might be useful in an important and representative phase of the engineering design process, that of design requirement development and capture.The paper consists of two parts. In the first part ontologies and their use are discussed, and a methodology for developing ontologies is explored. In the second part, three very different types of ontology are developed in accordance with the methodology. Each of the ontologies captures a different conceptual facet of the engineering design domain, described at a quite different level of abstraction than the others. The process of developing ontologies is illustrated in a practical way and the application of these ontologies for supporting the capture of the engineering design requirement is described as a means of demonstrating the general potential of ontologies.     

The International Society for the Study of Vascular Anomalies (ISSVA) ontology

The International Society for the Study of Vascular Anomalies (ISSVA) provides a classification for vascular anomalies that enables specialists to unambiguously classify diagnoses. This classification is only available in PDF format and is not machine-readable, nor does it provide unique identifiers that allow for structured registration. In this paper, we describe the process of transforming the ISSVA classification into an ontology. We also describe the structure of this ontology, as well as two applications of the ontology using examples from the domain of rare disease research. We used the expertise of an ontology expert and clinician during the development process. We semi-automatically added mappings to relevant external ontologies using automated ontology matching systems and manual assessment by experts. The ISSVA ontology should contribute to making data for vascular anomaly research more Findable, Accessible, Interoperable, and Reusable (FAIR). The ontology is available at https://bioportal.bioontology.org/ontologies/ISSVA.