Fast modularisation and aomic decomposition of ontologies using axiom dependency hypergraphs

In this paper we define the notion of an axiom dependency hypergraph, which explicitly represents how axioms are included into a module by the algorithm for computing locality-based modules. A locality-based module of an ontology corresponds to a set of connected nodes in the hypergraph, and atoms of an ontology to strongly connected components. Collapsing the strongly connected components into single nodes yields a condensed hypergraph that comprises a representation of the atomic decomposition of the ontology. To speed up the condensation of the hypergraph, we first reduce its size by collapsing the strongly connected components of its graph fragment employing a linear time graph algorithm. This approach helps to significantly reduce the time needed for computing the atomic decomposition of an ontology. We provide an experimental evaluation for computing the atomic decomposition of large biomedical ontologies. We also demonstrate a significant improvement in the time needed to extract locality-based modules from an axiom dependency hypergraph and its condensed version.

The relevance of perspectivism to the task of modularisation in ontology development

An ontology development methodology seeks to provide developers with established principles, processes, practices, methods and activities for developing ontologies (Gasevic et al., 2009). Diverse methodologies have been published for the development of ontologies, and have evolved, based on the diverse experiences of researchers and practitioners, and the development teams who surveyed the benefits and shortcomings of the available methodologies in order to determine the applicability of methodologies to particular contexts. An evaluation of existing ontology development methodologies has identified that the concept formulation process is not well defined, or based on rigorous processes (Castro et al., 2006; Winters & Tolk, 2009). In order for the validity of the social realism of the actors in a social setting to be captured, the perspectives of each actor needs to be acknowledged and incorporated into the concept formulation process / framework. This paper demonstrates how consideration of perspectivism leads to a meaningful modularisation of the resultant ontology.

Semantic network analysis of ontologies

A key argument for modeling knowledge in ontologies is the easy re-use and re-engineering of the knowledge. However, beside consistency checking, current ontology engineering tools provide only basic functionalities for analyzing ontologies. Since ontologies can be considered as (labeled, directed) graphs, graph analysis techniques are a suitable answer for this need. Graph analysis has been performed by sociologists for over 60 years, and resulted in the vivid research area of Social Network Analysis (SNA). While social network structures in general currently receive high attention in the Semantic Web community, there are only very few SNA applications up to now, and virtually none for analyzing the structure of ontologies. We illustrate in this paper the benefits of applying SNA to ontologies and the Semantic Web, and discuss which research topics arise on the edge between the two areas. In particular, we discuss how different notions of centrality describe the core content and structure of an ontology. From the rather simple notion of degree centrality over betweenness centrality to the more complex eigenvector centrality based on Hermitian matrices, we illustrate the insights these measures provide on two ontologies, which are different in purpose, scope, and size.

Application of ontologies in peer-to-peer database with routing queries based on ant colony algorithm

A significant set of information stored in different databases around the world, can be shared through peer-topeer databases. With that, is obtained a large base of knowledge, without the need for large investments because they are used existing databases, as well as the infrastructure in place. However, the structural characteristics of peer-topeer, makes complex the process of finding such information. On the other side, these databases are often heterogeneous in their schemas, but semantically similar in their content. A good peer-to-peer databases systems should allow the user access information from databases scattered across the network and receive only the information really relate to your topic of interest. This paper proposes to use ontologies in peer-to-peer database queries to represent the semantics inherent to the data. The main contribution of this work is enable integration between heterogeneous databases, improve the performance of such queries and use the algorithm of optimization Ant Colony to solve the problem of locating information on peer-to-peer networks, which presents an improve of 18% in results. © 2011 IEEE.

Combining statistical and semantic approaches to the translation of ontologies and taxonomies

Ontologies and taxonomies are widely used to organize concepts providing the basis for activities such as indexing, and as background knowledge for NLP tasks. As such, translation of these resources would prove useful to adapt these systems to new languages. However, we show that the nature of these resources is significantly different from the "free-text" paradigm used to train most statistical machine translation systems. In particular, we see significant differences in the linguistic nature of these resources and such resources have rich additional semantics. We demonstrate that as a result of these linguistic differences, standard SMT methods, in particular evaluation metrics, can produce poor performance. We then look to the task of leveraging these semantics for translation, which we approach in three ways: by adapting the translation system to the domain of the resource; by examining if semantics can help to predict the syntactic structure used in translation; and by evaluating if we can use existing translated taxonomies to disambiguate translations. We present some early results from these experiments, which shed light on the degree of success we may have with each approach

Strong Connectivity in Directed Hypergraphs and its Application to the Atomic Decomposition of Ontologies

Los hipergrafos dirigidos se han empleado en problemas relacionados con lógica proposicional, bases de datos relacionales, linguística computacional y aprendizaje automático. Los hipergrafos dirigidos han sido también utilizados como alternativa a los grafos (bipartitos) dirigidos para facilitar el estudio de las interacciones entre componentes de sistemas complejos que no pueden ser fácilmente modelados usando exclusivamente relaciones binarias. En este contexto, este tipo de representación es conocida como hiper-redes. Un hipergrafo dirigido es una generalización de un grafo dirigido especialmente adecuado para la representación de relaciones de muchos a muchos. Mientras que una arista en un grafo dirigido define una relación entre dos de sus nodos, una hiperarista en un hipergrafo dirigido define una relación entre dos conjuntos de sus nodos. La conexión fuerte es una relación de equivalencia que divide el conjunto de nodos de un hipergrafo dirigido en particiones y cada partición define una clase de equivalencia conocida como componente fuertemente conexo. El estudio de los componentes fuertemente conexos de un hipergrafo dirigido puede ayudar a conseguir una mejor comprensión de la estructura de este tipo de hipergrafos cuando su tamaño es considerable. En el caso de grafo dirigidos, existen algoritmos muy eficientes para el cálculo de los componentes fuertemente conexos en grafos de gran tamaño. Gracias a estos algoritmos, se ha podido averiguar que la estructura de la WWW tiene forma de “pajarita”, donde más del 70% del los nodos están distribuidos en tres grandes conjuntos y uno de ellos es un componente fuertemente conexo. Este tipo de estructura ha sido también observada en redes complejas en otras áreas como la biología. Estudios de naturaleza similar no han podido ser realizados en hipergrafos dirigidos porque no existe algoritmos capaces de calcular los componentes fuertemente conexos de este tipo de hipergrafos. En esta tesis doctoral, hemos investigado como calcular los componentes fuertemente conexos de un hipergrafo dirigido. En concreto, hemos desarrollado dos algoritmos para este problema y hemos determinado que son correctos y cuál es su complejidad computacional. Ambos algoritmos han sido evaluados empíricamente para comparar sus tiempos de ejecución. Para la evaluación, hemos producido una selección de hipergrafos dirigidos generados de forma aleatoria inspirados en modelos muy conocidos de grafos aleatorios como Erdos-Renyi, Newman-Watts-Strogatz and Barabasi-Albert. Varias optimizaciones para ambos algoritmos han sido implementadas y analizadas en la tesis. En concreto, colapsar los componentes fuertemente conexos del grafo dirigido que se puede construir eliminando ciertas hiperaristas complejas del hipergrafo dirigido original, mejora notablemente los tiempos de ejecucion de los algoritmos para varios de los hipergrafos utilizados en la evaluación. Aparte de los ejemplos de aplicación mencionados anteriormente, los hipergrafos dirigidos han sido también empleados en el área de representación de conocimiento. En concreto, este tipo de hipergrafos se han usado para el cálculo de módulos de ontologías. Una ontología puede ser definida como un conjunto de axiomas que especifican formalmente un conjunto de símbolos y sus relaciones, mientras que un modulo puede ser entendido como un subconjunto de axiomas de la ontología que recoge todo el conocimiento que almacena la ontología sobre un conjunto especifico de símbolos y sus relaciones. En la tesis nos hemos centrado solamente en módulos que han sido calculados usando la técnica de localidad sintáctica. Debido a que las ontologías pueden ser muy grandes, el cálculo de módulos puede facilitar las tareas de re-utilización y mantenimiento de dichas ontologías. Sin embargo, analizar todos los posibles módulos de una ontología es, en general, muy costoso porque el numero de módulos crece de forma exponencial con respecto al número de símbolos y de axiomas de la ontología. Afortunadamente, los axiomas de una ontología pueden ser divididos en particiones conocidas como átomos. Cada átomo representa un conjunto máximo de axiomas que siempre aparecen juntos en un modulo. La decomposición atómica de una ontología es definida como un grafo dirigido de tal forma que cada nodo del grafo corresponde con un átomo y cada arista define una dependencia entre una pareja de átomos. En esta tesis introducimos el concepto de“axiom dependency hypergraph” que generaliza el concepto de descomposición atómica de una ontología. Un modulo en una ontología correspondería con un componente conexo en este tipo de hipergrafos y un átomo de una ontología con un componente fuertemente conexo. Hemos adaptado la implementación de nuestros algoritmos para que funcionen también con axiom dependency hypergraphs y poder de esa forma calcular los átomos de una ontología. Para demostrar la viabilidad de esta idea, hemos incorporado nuestros algoritmos en una aplicación que hemos desarrollado para la extracción de módulos y la descomposición atómica de ontologías. A la aplicación la hemos llamado HyS y hemos estudiado sus tiempos de ejecución usando una selección de ontologías muy conocidas del área biomédica, la mayoría disponibles en el portal de Internet NCBO. Los resultados de la evaluación muestran que los tiempos de ejecución de HyS son mucho mejores que las aplicaciones más rápidas conocidas. ABSTRACT Directed hypergraphs are an intuitive modelling formalism that have been used in problems related to propositional logic, relational databases, computational linguistic and machine learning. Directed hypergraphs are also presented as an alternative to directed (bipartite) graphs to facilitate the study of the interactions between components of complex systems that cannot naturally be modelled as binary relations. In this context, they are known as hyper-networks. A directed hypergraph is a generalization of a directed graph suitable for representing many-to-many relationships. While an edge in a directed graph defines a relation between two nodes of the graph, a hyperedge in a directed hypergraph defines a relation between two sets of nodes. Strong-connectivity is an equivalence relation that induces a partition of the set of nodes of a directed hypergraph into strongly-connected components. These components can be collapsed into single nodes. As result, the size of the original hypergraph can significantly be reduced if the strongly-connected components have many nodes. This approach might contribute to better understand how the nodes of a hypergraph are connected, in particular when the hypergraphs are large. In the case of directed graphs, there are efficient algorithms that can be used to compute the strongly-connected components of large graphs. For instance, it has been shown that the macroscopic structure of the World Wide Web can be represented as a “bow-tie” diagram where more than 70% of the nodes are distributed into three large sets and one of these sets is a large strongly-connected component. This particular structure has been also observed in complex networks in other fields such as, e.g., biology. Similar studies cannot be conducted in a directed hypergraph because there does not exist any algorithm for computing the strongly-connected components of the hypergraph. In this thesis, we investigate ways to compute the strongly-connected components of directed hypergraphs. We present two new algorithms and we show their correctness and computational complexity. One of these algorithms is inspired by Tarjan’s algorithm for directed graphs. The second algorithm follows a simple approach to compute the stronglyconnected components. This approach is based on the fact that two nodes of a graph that are strongly-connected can also reach the same nodes. In other words, the connected component of each node is the same. Both algorithms are empirically evaluated to compare their performances. To this end, we have produced a selection of random directed hypergraphs inspired by existent and well-known random graphs models like Erd˝os-Renyi and Newman-Watts-Strogatz. Besides the application examples that we mentioned earlier, directed hypergraphs have also been employed in the field of knowledge representation. In particular, they have been used to compute the modules of an ontology. An ontology is defined as a collection of axioms that provides a formal specification of a set of terms and their relationships; and a module is a subset of an ontology that completely captures the meaning of certain terms as defined in the ontology. In particular, we focus on the modules computed using the notion of syntactic locality. As ontologies can be very large, the computation of modules facilitates the reuse and maintenance of these ontologies. Analysing all modules of an ontology, however, is in general not feasible as the number of modules grows exponentially in the number of terms and axioms of the ontology. Nevertheless, the modules can succinctly be represented using the Atomic Decomposition of an ontology. Using this representation, an ontology can be partitioned into atoms, which are maximal sets of axioms that co-occur in every module. The Atomic Decomposition is then defined as a directed graph such that each node correspond to an atom and each edge represents a dependency relation between two atoms. In this thesis, we introduce the notion of an axiom dependency hypergraph which is a generalization of the atomic decomposition of an ontology. A module in the ontology corresponds to a connected component in the hypergraph, and the atoms of the ontology to the strongly-connected components. We apply our algorithms for directed hypergraphs to axiom dependency hypergraphs and in this manner, we compute the atoms of an ontology. To demonstrate the viability of this approach, we have implemented the algorithms in the application HyS which computes the modules of ontologies and calculate their atomic decomposition. In the thesis, we provide an experimental evaluation of HyS with a selection of large and prominent biomedical ontologies, most of which are available in the NCBO Bioportal. HyS outperforms state-of-the-art implementations in the tasks of extracting modules and computing the atomic decomposition of these ontologies.

Semantic Search of Internet Information Resources on Base of Ontologies and Multilinguistic Thesauruses

The approaches to the analysis of various information resources pertinent to user requirements at a semantic level are determined by the thesauruses of the appropriate subject domains. The algorithms of formation and normalization of the multilinguistic thesaurus, and also methods of their comparison are given.

Networks of contextualised ontologies for the Semantic Web

Currently many ontologies are available for addressing different domains. However, it is not always possible to deploy such ontologies to support collaborative working, so that their full potential can be exploited to implement intelligent cooperative applications capable of reasoning over a network of context-specific ontologies. The main problem arises from the fact that presently ontologies are created in an isolated way to address specific needs. However we foresee the need for a network of ontologies which will support the next generation of intelligent applications/devices, and, the vision of Ambient Intelligence. The main objective of this paper is to motivate the design of a networked ontology (Meta) model which formalises ways of connecting available ontologies so that they are easy to search, to characterise and to maintain. The aim is to make explicit the virtual and implicit network of ontologies serving the Semantic Web.

The Current Landscape of Pitfalls in Ontologies

A growing number of ontologies are already available thanks to development initiatives in many different fields. In such ontology developments, developers must tackle a wide range of difficulties and handicaps, which can result in the appearance of anomalies in the resulting ontologies. Therefore, ontology evaluation plays a key role in ontology development projects. OOPS! is an on-line tool that automatically detects pitfalls, considered as potential errors or problems, and thus may help ontology developers to improve their ontologies. To gain insight in the existence of pitfalls and to assess whether there are differences among ontologies developed by novices, a random set of already scanned ontologies, and existing well-known ones, data of 406 OWL ontologies were analysed on OOPS!’s 21 pitfalls, of which 24 ontologies were also examined manually on the detected pitfalls. The various analyses performed show only minor differences between the three sets of ontologies, therewith providing a general landscape of pitfalls in ontologies.

Ontologies for crisis management:a review of state of the art in ontology design and usability

The growing use of a variety of information systems in crisis management both by non-governmental organizations (NGOs) and emergency management agencies makes the challenges of information sharing and interoperability increasingly important. The use of semantic web technologies is a growing area and is a technology stack specifically suited to these challenges. This paper presents a review of ontologies, vocabularies and taxonomies that are useful in crisis management systems. We identify the different subject areas relevant to crisis management based on a review of the literature. The different ontologies and vocabularies available are analysed in terms of their coverage, design and usability. We also consider the use cases for which they were designed and the degree to which they follow a variety of standards. While providing comprehensive ontologies for the crisis domain is not feasible or desirable there is considerable scope to develop ontologies for the subject areas not currently covered and for the purposes of interoperability.

An Analysis of Some Relations Among Domain Ontologies

* This paper was made according to the program of fundamental scientific research of the Presidium of the Russian Academy of Sciences «Mathematical simulation and intellectual systems», the project "Theoretical foundation of the intellectual systems based on ontologies for intellectual support of scientific researches".

dynamic evolutions based on ontologies

With the continuous changes in application requirements of the enterprises, Web resources must be updated, so do the underlying ontologies that are associated with the Web resources. In the situation, it is very challenging for ontological engineers to specify the changes of ontologies, keep their consistencies and achieve semantic query of Web resources based on the evolving ontologies. We propose a construct called Prioritized Knowledge Base (PKB) based on SHOQ(D) description logic, and discuss some properties of PKB.PKB can be used for describing the evolutions and updates of ontologies with conflicting information. Furthermore, we develop some algorithms for checking conflict rules and performing semantic query based on PKB.

A Data Model for Content Modelling of Temporal Media

This paper describes a data model for content representation of temporal media in an IP based sensor network. The model is formed by introducing the idea of semantic-role from linguistics into the underlying concepts of formal event representation with the aim of developing a common event model. The architecture of a prototype system for a multi camera surveillance system, based on the proposed model is described. The important aspects of the proposed model are its expressiveness, its ability to model content of temporal media, and its suitability for use with a natural language interface. It also provides a platform for temporal information fusion, as well as organizing sensor annotations by help of ontologies.

Ontologies for reusing data cleaning knowledge

The emergence of new business models, namely, the establishment of partnerships between organizations, the chance that companies have of adding existing data on the web, especially in the semantic web, to their information, led to the emphasis on some problems existing in databases, particularly related to data quality. Poor data can result in loss of competitiveness of the organizations holding these data, and may even lead to their disappearance, since many of their decision-making processes are based on these data. For this reason, data cleaning is essential. Current approaches to solve these problems are closely linked to database schemas and specific domains. In order that data cleaning can be used in different repositories, it is necessary for computer systems to understand these data, i.e., an associated semantic is needed. The solution presented in this paper includes the use of ontologies: (i) for the specification of data cleaning operations and, (ii) as a way of solving the semantic heterogeneity problems of data stored in different sources. With data cleaning operations defined at a conceptual level and existing mappings between domain ontologies and an ontology that results from a database, they may be instantiated and proposed to the expert/specialist to be executed over that database, thus enabling their interoperability.

Creation and merging of ontology top-levels

We provide a new method for systematically structuring the top-down level of ontologies. It is based on an interactive, top-down knowledge acquisition process, which assures that the knowledge engineer considers all possible cases while avoiding redundant acquisition. The method is suited especially for creating/merging the top part(s) of the ontologies, where high accuracy is required, and for supporting the merging of two (or more) ontologies on that level.