Application of Semantics to Solve Problems in Life Sciences

Fecha de lectura de Tesis: 10 de diciembre de 2018La cantidad de información que se genera en la Web se ha incrementado en los últimos años. La mayor parte de esta información se encuentra accesible en texto, siendo el ser humano el principal usuario de la Web. Sin embargo, a pesar de todos los avances producidos en el área del procesamiento del lenguaje natural, los ordenadores tienen problemas para procesar esta información textual. En este cotexto, existen dominios de aplicación en los que se están publicando grandes cantidades de información disponible como datos estructurados como en el área de las Ciencias de la Vida. El análisis de estos datos es de vital importancia no sólo para el avance de la ciencia, sino para producir avances en el ámbito de la salud. Sin embargo, estos datos están localizados en diferentes repositorios y almacenados en diferentes formatos que hacen difícil su integración. En este contexto, el paradigma de los Datos Vinculados como una tecnología que incluye la aplicación de algunos estándares propuestos por la comunidad W3C tales como HTTP URIs, los estándares RDF y OWL. Haciendo uso de esta tecnología, se ha desarrollado esta tesis doctoral basada en cubrir los siguientes objetivos principales: 1) promover el uso de los datos vinculados por parte de la comunidad de usuarios del ámbito de las Ciencias de la Vida 2) facilitar el diseño de consultas SPARQL mediante el descubrimiento del modelo subyacente en los repositorios RDF 3) crear un entorno colaborativo que facilite el consumo de Datos Vinculados por usuarios finales, 4) desarrollar un algoritmo que, de forma automática, permita descubrir el modelo semántico en OWL de un repositorio RDF, 5) desarrollar una representación en OWL de ICD-10-CM llamada Dione que ofrezca una metodología automática para la clasificación de enfermedades de pacientes y su posterior validación haciendo uso de un razonador OWL

Ontology Alignment at the Instance and Schema Level

We present PARIS, an approach for the automatic alignment of ontologies. PARIS aligns not only instances, but also relations and classes. Alignments at the instance-level cross-fertilize with alignments at the schema-level. Thereby, our system provides a truly holistic solution to the problem of ontology alignment. The heart of the approach is probabilistic. This allows PARIS to run without any parameter tuning. We demonstrate the efficiency of the algorithm and its precision through extensive experiments. In particular, we obtain a precision of around 90% in experiments with two of the world's largest ontologies.Comment: Technical Report at INRIA RT-040

An ontological approach to logistics

In today’s global market, the competitiveness of enterprises is strongly dictated by their ability to collaborate with other enterprises. Ontologies enable common understanding of concepts and have been acknowledged as a powerful means to foster collaboration, both within the boundaries of an individual enterprise (intra-enterprise) as outside these boundaries (inter-enterprise). This paper argues that the use of ontologies can be beneficial for enterprise interoperability in the logistics domain, to improve communication and foster knowledge reuse, to facilitate the integration of existing systems and to support the development process of software solutions. Our experience shows that the development of ontologies for logistics is not a trivial task, and guidelines and best practices are necessary in this domain, especially to bridge the gap between theory and practice. On the one hand, proper theoretical and methodological support for ontology engineering is necessary in order to deliver precise, consistent and well-founded solutions to the market. On the other hand, solutions to practical issues should be provided and not take too long to be produced in order not to be detached from the original real market needs. This paper proposes an ontological approach for logistics that balances the trade-off between precision and pragmatism, by combining top-down and bottom-up practices for ontology engineering. From a top-down perspective, we promote the reuse of existing general-purpose (upper) ontologies and specialize them for the purpose of logistics. From a bottom-up perspective, we reuse code lists and classifications that already exist in logistics to support the creation of instances of our upper level concepts. The paper also presents a representative fragment of our core ontology for logistics and identifies areas for further work in ontology engineering for logistics

Mapping and Merging of Anatomical Ontologies

This article presents the principal results of the Ph.D. thesis Intelligent systems in bioinformatics: mapping and merging anatomical ontologies by Peter Petrov, successfully defended at the St. Kliment Ohridski University of Sofia, Faculty of Mathematics and Informatics, Department of Information Technologies, on 26 April 2013.The problem of mapping and merging ontologies in general is an important one in the area of ontology engineering. The same problem considered within the narrower area of anatomical ontologies (AOs) is important in bioinformatics because solving it could enable the transfer of data and the application of knowledge obtained from various model organisms to other model and non-model organisms, and even to research areas such as those of human health and medicine. This paper presents a detailed summary of the author’s PhD research done in the period 2007–2013. The paper’s main topic is the problem of mapping and merging of multiple species-specific AOs and the related approaches, methods, and procedures that can be used for solving it. ACM Computing Classification System (1998): J.3, E.1, G.2.2, G.2.3, I.2.1, I.2.4

Automatic service categorisation through machine learning in emergent middleware

The modern environment of mobile, pervasive, evolving services presents a great challenge to traditional solutions for enabling interoperability. Automated solutions appear to be the only way to achieve interoperability with the needed level of flexibility and scalability. While necessary, the techniques used to determine compatibility, as a precursor to interaction, come at a substantial computational cost, especially when checks are performed between systems in unrelated domains. To overcome this, we apply machine learning to extract high-level functionality information through text categorisation of a system's interface description. This categorisation allows us to restrict the scope of compatibility checks, giving an overall performance gain when conducting matchmaking between systems. We have evaluated our approach on a corpus of web service descriptions, where even with moderate categorisation accuracy, a substantial performance benefit can be found. This in turn improves the applicability of our overall approach for achieving interoperability in the Connect project

Enrichment and ranking of the YouTube tag space and integration with the Linked Data cloud

The increase of personal digital cameras with video functionality and video-enabled camera phones has increased the amount of user-generated videos on the Web. People are spending more and more time viewing online videos as a major source of entertainment and “infotainment”. Social websites allow users to assign shared free-form tags to user-generated multimedia resources, thus generating annotations for objects with a minimum amount of effort. Tagging allows communities to organise their multimedia items into browseable sets, but these tags may be poorly chosen and related tags may be omitted. Current techniques to retrieve, integrate and present this media to users are deficient and could do with improvement. In this paper, we describe a framework for semantic enrichment, ranking and integration of web video tags using Semantic Web technologies. Semantic enrichment of folksonomies can bridge the gap between the uncontrolled and flat structures typically found in user-generated content and structures provided by the Semantic Web. The enhancement of tag spaces with semantics has been accomplished through two major tasks: a tag space expansion and ranking step; and through concept matching and integration with the Linked Data cloud. We have explored social, temporal and spatial contexts to enrich and extend the existing tag space. The resulting semantic tag space is modelled via a local graph based on co-occurrence distances for ranking. A ranked tag list is mapped and integrated with the Linked Data cloud through the DBpedia resource repository. Multi-dimensional context filtering for tag expansion means that tag ranking is much easier and it provides less ambiguous tag to concept matching

Semantics-aware planning methodology for automatic web service composition

Service-Oriented Computing (SOC) has been a major research topic in the past years. It is based on the idea of composing distributed applications even in heterogeneous environments by discovering and invoking network-available Web Services to accomplish some complex tasks when no existing service can satisfy the user request. Service-Oriented Architecture (SOA) is a key design principle to facilitate building of these autonomous, platform-independent Web Services. However, in distributed environments, the use of services without considering their underlying semantics, either functional semantics or quality guarantees can negatively affect a composition process by raising intermittent failures or leading to slow performance. More recently, Artificial Intelligence (AI) Planning technologies have been exploited to facilitate the automated composition. But most of the AI planning based algorithms do not scale well when the number of Web Services increases, and there is no guarantee that a solution for a composition problem will be found even if it exists. AI Planning Graph tries to address various limitations in traditional AI planning by providing a unique search space in a directed layered graph. However, the existing AI Planning Graph algorithm only focuses on finding complete solutions without taking account of other services which are not achieving the goals. It will result in the failure of creating such a graph in the case that many services are available, despite most of them being irrelevant to the goals. This dissertation puts forward a concept of building a more intelligent planning mechanism which should be a combination of semantics-aware service selection and a goal-directed planning algorithm. Based on this concept, a new planning system so-called Semantics Enhanced web service Mining (SEwsMining) has been developed. Semantic-aware service selection is achieved by calculating on-demand multi-attributes semantics similarity based on semantic annotations (QWSMO-Lite). The planning algorithm is a substantial revision of the AI GraphPlan algorithm. To reduce the size of planning graph, a bi-directional planning strategy has been developed

Knowledge Base Enrichment by Relation Learning from Social Tagging Data

There has been considerable interest in transforming unstructured social tagging data into structured knowledge for semantic-based retrieval and recommendation. Research in this line mostly exploits data co-occurrence and often overlooks the complex and ambiguous meanings of tags. Furthermore, there have been few comprehensive evaluation studies regarding the quality of the discovered knowledge. We propose a supervised learning method to discover subsumption relations from tags. The key to this method is quantifying the probabilistic association among tags to better characterise their relations. We further develop an algorithm to organise tags into hierarchies based on the learned relations. Experiments were conducted using a large, publicly available dataset, Bibsonomy, and three popular, human-engineered or data-driven knowledge bases: DBpedia, Microsoft Concept Graph, and ACM Computing Classification System. We performed a comprehensive evaluation using different strategies: relation-level, ontology-level, and knowledge base enrichment based evaluation. The results clearly show that the proposed method can extract knowledge of better quality than the existing methods against the gold standard knowledge bases. The proposed approach can also enrich knowledge bases with new subsumption relations, having the potential to significantly reduce time and human effort for knowledge base maintenance and ontology evolution