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

A Survey of Volunteered Open Geo-Knowledge Bases in the Semantic Web

Over the past decade, rapid advances in web technologies, coupled with innovative models of spatial data collection and consumption, have generated a robust growth in geo-referenced information, resulting in spatial information overload. Increasing 'geographic intelligence' in traditional text-based information retrieval has become a prominent approach to respond to this issue and to fulfill users' spatial information needs. Numerous efforts in the Semantic Geospatial Web, Volunteered Geographic Information (VGI), and the Linking Open Data initiative have converged in a constellation of open knowledge bases, freely available online. In this article, we survey these open knowledge bases, focusing on their geospatial dimension. Particular attention is devoted to the crucial issue of the quality of geo-knowledge bases, as well as of crowdsourced data. A new knowledge base, the OpenStreetMap Semantic Network, is outlined as our contribution to this area. Research directions in information integration and Geographic Information Retrieval (GIR) are then reviewed, with a critical discussion of their current limitations and future prospects

Social, Structured and Semantic Search

International audienceSocial content such as blogs, tweets, news etc. is a rich source of interconnected information. We identify a set of requirements for the meaningful exploitation of such rich content, and present a new data model, called S3, which is the first to satisfy them. S3 captures social relationships between users, and between users and content, but also the structure present in rich social content, as well as its semantics. We provide the first top-k keyword search algorithm taking into account the social, structured, and semantic dimensions and formally establish its termination and correctness. Experiments on real social networks demonstrate the efficiency and qualitative advantage of our algorithm through the joint exploitation of the social, structured, and semantic dimensions of S3

Schema-aware keyword search on linked data

Keyword search is a popular technique for querying the ever growing repositories of RDF graph data on the Web. This is due to the fact that the users do not need to master complex query languages (e.g., SQL, SPARQL) and they do not need to know the underlying structure of the data on the Web to compose their queries. Keyword search is simple and flexible. However, it is at the same time ambiguous since a keyword query can be interpreted in different ways. This feature of keyword search poses at least two challenges: (a) identifying relevant results among a multitude of candidate results, and (b) dealing with the performance scalability issue of the query evaluation algorithms. In the literature, multiple schema-unaware approaches are proposed to cope with the above challenges. Some of them identify as relevant results only those candidate results which maintain the keyword instances in close proximity. Other approaches filter out irrelevant results using their structural characteristics or rank and top-k process the retrieved results based on statistical information about the data. In any case, these approaches cannot disambiguate the query to identify the intent of the user and they cannot scale satisfactorily when the size of the data and the number of the query keywords grow. In recent years, different approaches tried to exploit the schema (structural summary) of the RDF (Resource Description Framework) data graph to address the problems above. In this context, an original hierarchical clustering technique is introduced in this dissertation. This approach clusters the results based on a semantic interpretation of the keyword instances and takes advantage of relevance feedback from the user. The clustering hierarchy uses pattern graphs which are structured queries and clustering together result graphs with the same structure. Pattern graphs represent possible interpretations for the keyword query. By navigating though the hierarchy the user can select the pattern graph which is relevant to her intent. Nevertheless, structural summaries are approximate representations of the data and, therefore, might return empty answers or miss results which are relevant to the user intent. To address this issue, a novel approach is presented which combines the use of the structural summary and the user feedback with a relaxation technique for pattern graphs to extract additional results potentially of interest to the user. Query caching and multi-query optimization techniques are leveraged for the efficient evaluation of relaxed pattern graphs. Although the approaches which consider the structural summary of the data graph are promising, they require interaction with the user. It is claimed in this dissertation that without additional information from the user, it is not possible to produce results of high quality from keyword search on RDF data with the existing techniques. In this regard, an original keyword query language on RDF data is introduced which allows the user to convey his intention flexibly and effortlessly by specifying cohesive keyword groups. A cohesive group of keywords in a query indicates that its keywords should form a cohesive unit in the query results. It is experimentally demonstrated that cohesive keyword queries improve the result quality effectively and prune the search space of the pattern graphs efficiently compared to traditional keyword queries. Most importantly, these benefits are achieved while retaining the simplicity and the convenience of traditional keyword search. The last issue addressed in this dissertation is the diversification problem for keyword search on RDF data. The goal of diversification is to trade off relevance and diversity in the results set of a keyword query in order to minimize the dissatisfaction of the average user. Novel metrics are developed for assessing relevance and diversity along with techniques for the generation of a relevant and diversified set of query interpretations for a keyword query on an RDF data graph. Experimental results show the effectiveness of the metrics and the efficiency of the approach

Developing Knowledge Models of Social Media: A Case Study on LinkedIn

User Generated Content (UGC) exchanged via large Social Network is considered a very important knowledge source about all aspects of the social engagements (e.g. interests, events, personal information, personal preferences, social experience, skills etc.). However this data is inherently unstructured or semi-structured. In this paper, we describe the results of a case study on LinkedIn Ireland public profiles. The study investigated how the available knowledge could be harvested from LinkedIn in a novel way by developing and applying a reusable knowledge model using linked open data vocabularies and semantic web. In addition, the paper discusses the crawling and data normalisation strategies that we developed, so that high quality metadata could be extracted from the LinkedIn public profiles. Apart from the search engine in LinkedIn.com itself, there are no well known publicly available endpoints that allow users to query knowledge concerning the interests of individuals on LinkedIn. In particular, we present a system that extracts and converts information from raw web pages of LinkedIn public profiles into a machine-readable, interoperable format using data mining and Semantic Web technologies. The outcomes of our research can be summarized as follows: (1) A reusable knowledge model which can represent LinkedIn public users and company profiles using linked data vocabularies and structured data, (2) a public SPARQL endpoint to access structured data about Irish industry and public profiles, (3) a scalable data crawling strategy and mashup based data normalisation approach. The proposed data mining and knowledge representation proposed in this paper are evaluated in four ways: (1) We evaluate metadata quality using automated techniques, such as data completeness and data linkage. (2) Data accuracy is evaluated via user studies. In particular, accuracy is evaluated by comparison of manually entered metadata fields and the metadata which was automatically extracted. (3) User perceived metadata quality is measured by asking users to rate the automatically extracted metadata in user studies. (4) Finally, the paper discusses how the extracted metadata suits for a user interface design. Overall, the evaluations show that the extracted metadata is of high quality and meets the requirements of a data visualisation user interface

Interlinking educational data to web of data

With the proliferation of educational data on the Web, publishing and interlinking eLearning resources have become an important issue nowadays. Educational resources are exposed under heterogeneous Intellectual Property Rights (IPRs) in different times and formats. Some resources are implicitly related to each other or to the interest, cultural and technical environment of learners. Linking educational resources to useful knowledge on the Web improves resource seeking. This becomes crucial for moving from current isolated eLearning repositories towards an open discovery space, including distributed resources irrespective of their geographic and system boundaries. Linking resources is also useful for enriching educational content, as it provides a richer context and other related information to both educators and learners. On the other hand, the emergence of the so-called "Linked Data" brings new opportunities for interconnecting different kinds of resources on the Web of Data. Using the Linked Data approach, data providers can publish structured data and establish typed links between them from various sources. To this aim, many tools, approaches and frameworks have been built to first expose the data as Linked Data formats and to second discover the similarities between entities in the datasets. The research carried out for this PhD thesis assesses the possibilities of applying the Linked Open Data paradigm to the enrichment of educational resources. Generally speaking, we discuss the interlinking educational objects and eLearning resources on the Web of Data focusing on existing schemas and tools. The main goals of this thesis are thus to cover the following aspects: -- Exposing the educational (meta)data schemas and particularly IEEE LOM as Linked Data -- Evaluating currently available interlinking tools in the Linked Data context -- Analyzing datasets in the Linked Open Data cloud, to discover appropriate datasets for interlinking -- Discussing the benefits of interlinking educational (meta)data in practice