Large Scale Data Analytics with Language Integrated Query

Databases can easily reach petabytes (1,048,576 gigabytes) in scale. A system to enable users to efficiently retrieve or query data from multiple databases simultaneously is needed. This research introduces a new, cloud-based query framework, designed and built using Language Integrated Query, to query existing data sources without the need to integrate or restructure existing databases. Protein data obtained through the query framework proves its feasibility and cost effectiveness

Word Sense Disambiguation for Ontology Learning

Ontology learning aims to automatically extract ontological concepts and relationships from related text repositories and is expected to be more efficient and scalable than manual ontology development. One of the challenging issues associated with ontology learning is word sense disambiguation (WSD). Most WSD research employs resources such as WordNet, text corpora, or a hybrid approach. Motivated by the large volume and richness of user-generated content in social media, this research explores the role of social media in ontology learning. Specifically, our approach exploits social media as a dynamic context rich data source for WSD. This paper presents a method and preliminary evidence for the efficacy of our proposed method for WSD. The research is in progress toward conducting a formal evaluation of the social media based method for WSD, and plans to incorporate the WSD routine into an ontology learning system in the future

Search improvement within the geospatial web in the context of spatial data infrastructures

El trabajo desarrollado en esta tesis doctoral demuestra que es posible mejorar la búsqueda en el contexto de las Infraestructuras de Datos Espaciales mediante la aplicación de técnicas y buenas prácticas de otras comunidades científicas, especialmente de las comunidades de la Web y de la Web Semántica (por ejemplo, Linked Data). El uso de las descripciones semánticas y las aproximaciones basadas en el contenido publicado por la comunidad geoespacial pueden ayudar en la búsqueda de información sobre los fenómenos geográficos, y en la búsqueda de recursos geoespaciales en general. El trabajo comienza con un análisis de una aproximación para mejorar la búsqueda de las entidades geoespaciales desde la perspectiva de geocodificación tradicional. La arquitectura de geocodificación compuesta propuesta en este trabajo asegura una mejora de los resultados de geocodificación gracias a la utilización de diferentes proveedores de información geográfica. En este enfoque, el uso de patrones estructurales de diseño y ontologías en esta aproximación permite una arquitectura avanzada en términos de extensibilidad, flexibilidad y adaptabilidad. Además, una arquitectura basada en la selección de servicio de geocodificación permite el desarrollo de una metodología de la georreferenciación de diversos tipos de información geográfica (por ejemplo, direcciones o puntos de interés). A continuación, se presentan dos aplicaciones representativas que requieren una caracterización semántica adicional de los recursos geoespaciales. El enfoque propuesto en este trabajo utiliza contenidos basados en heurísticas para el muestreo de un conjunto de recursos geopesaciales. La primera parte se dedica a la idea de la abstracción de un fenómeno geográfico de su definición espacial. La investigación muestra que las buenas prácticas de la Web Semántica se puede reutilizar en el ámbito de una Infraestructura de Datos Espaciales para describir los servicios geoespaciales estandarizados por Open Geospatial Consortium por medio de geoidentificadores (es decir, por medio de las entidades de una ontología geográfica). La segunda parte de este capítulo desglosa la aquitectura y componentes de un servicio de geoprocesamiento para la identificación automática de ortoimágenes ofrecidas a través de un servicio estándar de publicación de mapas (es decir, los servicios que siguen la especificación OGC Web Map Service). Como resultado de este trabajo se ha propuesto un método para la identificación de los mapas ofrecidos por un Web Map Service que son ortoimágenes. A continuación, el trabajo se dedica al análisis de cuestiones relacionadas con la creación de los metadatos de recursos de la Web en el contexto del dominio geográfico. Este trabajo propone una arquitectura para la generación automática de conocimiento geográfico de los recursos Web. Ha sido necesario desarrollar un método para la estimación de la cobertura geográfica de las páginas Web. Las heurísticas propuestas están basadas en el contenido publicado por os proveedores de información geográfica. El prototipo desarrollado es capaz de generar metadatos. El modelo generado contiene el conjunto mínimo recomendado de elementos requeridos por un catálogo que sigue especificación OGC Catalogue Service for the Web, el estandar recomendado por deiferentes Infraestructuras de Datos Espaciales (por ejemplo, the Infrastructure for Spatial Information in the European Community (INSPIRE)). Además, este estudio determina algunas características de la Web Geoespacial actual. En primer lugar, ofrece algunas características del mercado de los proveedores de los recursos Web de la información geográfica. Este estudio revela algunas prácticas de la comunidad geoespacial en la producción de metadatos de las páginas Web, en particular, la falta de metadatos geográficos. Todo lo anterior es la base del estudio de la cuestión del apoyo a los usuarios no expertos en la búsqueda de recursos de la Web Geoespacial. El motor de búsqueda dedicado a la Web Geoespacial propuesto en este trabajo es capaz de usar como base un motor de búsqueda existente. Por otro lado, da soporte a la búsqueda exploratoria de los recursos geoespaciales descubiertos en la Web. El experimento sobre la precisión y la recuperación ha demostrado que el prototipo desarrollado en este trabajo es al menos tan bueno como el motor de búsqueda remoto. Un estudio dedicado a la utilidad del sistema indica que incluso los no expertos pueden realizar una tarea de búsqueda con resultados satisfactorios

BlogForever D2.4: Weblog spider prototype and associated methodology

The purpose of this document is to present the evaluation of different solutions for capturing blogs, established methodology and to describe the developed blog spider prototype

Table-to-Text: Generating Descriptive Text for Scientific Tables from Randomized Controlled Trials

Unprecedented amounts of data have been generated in the biomedical domain, and the bottleneck for biomedical research has shifted from data generation to data management, interpretation, and communication. Therefore, it is highly desirable to develop systems to assist in text generation from biomedical data, which will greatly improve the dissemination of scientific findings. However, very few studies have investigated issues of data-to-text generation in the biomedical domain. Here I present a systematic study for generating descriptive text from tables in randomized clinical trials (RCT) articles, which includes: (1) an information model for representing RCT tables; (2) annotated corpora containing pairs of RCT table and descriptive text, and labeled structural and semantic information of RCT tables; (3) methods for recognizing structural and semantic information of RCT tables; (4) methods for generating text from RCT tables, evaluated by a user study on three aspects: relevance, grammatical quality, and matching. The proposed hybrid text generation method achieved a low bilingual evaluation understudy (BLEU) score of 5.69; but human review achieved scores of 9.3, 9.9 and 9.3 for relevance, grammatical quality and matching, respectively, which are comparable to review of original human-written text. To the best of our knowledge, this is the first study to generate text from scientific tables in the biomedical domain. The proposed information model, labeled corpora and developed methods for recognizing tables and generating descriptive text could also facilitate other biomedical and informatics research and applications

Towards Constructing a Corpus for Studying the Effects of Treatments and Substances Reported in PubMed Abstracts

We present the construction of an annotated corpus of PubMed abstracts reporting about positive, negative or neutral effects of treatments or substances. Our ultimate goal is to annotate one sentence (rationale) for each abstract and to use this resource as a training set for text classification of effects discussed in PubMed abstracts. Currently, the corpus consists of 750 abstracts. We describe the automatic processing that supports the corpus construction, the manual annotation activities and some features of the medical language in the abstracts selected for the annotated corpus. It turns out that recognizing the terminology and the abbreviations is key for determining the rationale sentence. The corpus will be applied to improve our classifier, which currently has accuracy of 78.80% achieved with normalization of the abstract terms based on UMLS concepts from specific semantic groups and an SVM with a linear kernel. Finally, we discuss some other possible applications of this corpus.Comment: medical relation extraction, rationale extraction, effects and treatments, bioNL

Named Entity Recognition for Bacterial Type IV Secretion Systems

Research on specialized biological systems is often hampered by a lack of consistent terminology, especially across species. In bacterial Type IV secretion systems genes within one set of orthologs may have over a dozen different names. Classifying research publications based on biological processes, cellular components, molecular functions, and microorganism species should improve the precision and recall of literature searches allowing researchers to keep up with the exponentially growing literature, through resources such as the Pathosystems Resource Integration Center (PATRIC, patricbrc.org). We developed named entity recognition (NER) tools for four entities related to Type IV secretion systems: 1) bacteria names, 2) biological processes, 3) molecular functions, and 4) cellular components. These four entities are important to pathogenesis and virulence research but have received less attention than other entities, e.g., genes and proteins. Based on an annotated corpus, large domain terminological resources, and machine learning techniques, we developed recognizers for these entities. High accuracy rates (>80%) are achieved for bacteria, biological processes, and molecular function. Contrastive experiments highlighted the effectiveness of alternate recognition strategies; results of term extraction on contrasting document sets demonstrated the utility of these classes for identifying T4SS-related documents

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

The BLue Amazon Brain (BLAB): A Modular Architecture of Services about the Brazilian Maritime Territory

We describe the first steps in the development of an artificial agent focused on the Brazilian maritime territory, a large region within the South Atlantic also known as the Blue Amazon. The "BLue Amazon Brain" (BLAB) integrates a number of services aimed at disseminating information about this region and its importance, functioning as a tool for environmental awareness. The main service provided by BLAB is a conversational facility that deals with complex questions about the Blue Amazon, called BLAB-Chat; its central component is a controller that manages several task-oriented natural language processing modules (e.g., question answering and summarizer systems). These modules have access to an internal data lake as well as to third-party databases. A news reporter (BLAB-Reporter) and a purposely-developed wiki (BLAB-Wiki) are also part of the BLAB service architecture. In this paper, we describe our current version of BLAB's architecture (interface, backend, web services, NLP modules, and resources) and comment on the challenges we have faced so far, such as the lack of training data and the scattered state of domain information. Solving these issues presents a considerable challenge in the development of artificial intelligence for technical domains