Improving discovery in the life sciences using semantic Web technologies and linked data: design principles for life sciences knowledge organization systems

Dissertation presented to obtain the Ph.D degree in Bioinformatics

Combining open and closed world reasoning for the semantic web

Dissertação para obtenção do Grau de Doutor em Informática

Culture boundaries in semantic web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Hypermedia-based Web Services as System Integrators

As we move more closely to the practical concept of the Internet of Things and, our reliance on public and private APIs increases, web services and their related topics have become utterly crucial to the informatics community. However, the question about which style of web services would best solve a particular problem, can raise signi cant and multifarious debates. There can be found two implementation styles that highlight themselves: the RPC-oriented style represented by the SOAP protocol’s implementations and the hypermedia style, which is represented by the REST architectural style’s implementations. As we search examples of already established web services, we can nd a handful of robust and reliable public and private SOAP APIs, nevertheless, it seems that RESTful services are gaining popularity in the enterprise community. For the current generation of developers that work on informatics solutions, REST seems to represent a fundamental and straightforward alternative and even, a more deep-rooted approach than SOAP. But are they comparable? Do both approaches have each speci c best suitable scenarios? Such study is brie y carried out in the present document’s chapters, starting with the respective background study, following an analysis of the hypermedia approach and an instantiation of its architecture, in a particular case study applied in a BPM context.

Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Semantic web approach for dealing with administrative boundary revisions: a case study of Dhaka City

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Dynamic adaptation of interaction models for stateful web services

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Efficient paraconsistent reasoning with rules and ontologies for the semantic web

Ontologies formalized by means of Description Logics (DLs) and rules in the form of Logic Programs (LPs) are two prominent formalisms in the field of Knowledge Representation and Reasoning. While DLs adhere to the OpenWorld Assumption and are suited for taxonomic reasoning, LPs implement reasoning under the Closed World Assumption, so that default knowledge can be expressed. However, for many applications it is useful to have a means that allows reasoning over an open domain and expressing rules with exceptions at the same time. Hybrid MKNF knowledge bases make such a means available by formalizing DLs and LPs in a common logic, the Logic of Minimal Knowledge and Negation as Failure (MKNF). Since rules and ontologies are used in open environments such as the Semantic Web, inconsistencies cannot always be avoided. This poses a problem due to the Principle of Explosion, which holds in classical logics. Paraconsistent Logics offer a solution to this issue by assigning meaningful models even to contradictory sets of formulas. Consequently, paraconsistent semantics for DLs and LPs have been investigated intensively. Our goal is to apply the paraconsistent approach to the combination of DLs and LPs in hybrid MKNF knowledge bases. In this thesis, a new six-valued semantics for hybrid MKNF knowledge bases is introduced, extending the three-valued approach by Knorr et al., which is based on the wellfounded semantics for logic programs. Additionally, a procedural way of computing paraconsistent well-founded models for hybrid MKNF knowledge bases by means of an alternating fixpoint construction is presented and it is proven that the algorithm is sound and complete w.r.t. the model-theoretic characterization of the semantics. Moreover, it is shown that the new semantics is faithful w.r.t. well-studied paraconsistent semantics for DLs and LPs, respectively, and maintains the efficiency of the approach it extends.

Entwicklung eines Geschäftsmodells für verteilte ERP-Systeme auf Basis von Web Services

Magdeburg, Univ., Fak. für Informatik, Diss., 2012

Arquitectura corporativa de web services

Este proyecto consiste en la realización de un sistema informático que se encargue de ampliar la red comercial de una compañía de seguros a través de Internet. Para ello se utiliza la tecnología de web services, que nos permite efectuar transacciones de datos de manera rápida, fiable y segura. El web service que se ha diseñado se encarga de resolver y dar respuesta tanto a peticiones de solicitud de precios como de emisión de pólizas en varios ramos. El objetivo es ofrecer al cliente final un método sencillo y próximo de cotización y emisión de seguros.

MAPI: towards the integrated exploitation of bioinformatics Web Services.

BACKGROUND. Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. RESULTS. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. CONCLUSIONS. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

Enterprise semantic Web

This document is a journey through Semantic Web principles and Microsoft SharePoint in order to come to understand some advantages and disadvantages of theirs, and how Semantic Web principles can be blended into an enterprise solution like Microsoft SharePoint.

Towards a User-Friendly Platform for Building Language Resources based on Web Services

This paper presents the platform developed in the PANACEA project, a distributed factory that automates the stages involved in the acquisition, production, updating and maintenance of Language Resources required by Machine Translation and other Language Technologies. We adopt a set of tools that have been successfully used in the Bioinformatics field, they are adapted to the needs of our field and used to deploy web services, which can be combined to build more complex processing chains (workflows). This paper describes the platform and its different components (web services, registry, workflows, social network and interoperability). We demonstrate the scalability of the platform by carrying out a set of massive data experiments. Finally, a validation of the platform across a set of required criteria proves its usability for different types of users (non-technical users and providers).

Semantic web adoption: online tools for web evaluation and metadata extraction

This work briefly analyses the difficulties to adopt the Semantic Web, and in particular proposes systems to know the present level of migration to the different technologies that make up the Semantic Web. It focuses on the presentation and description of two tools, DigiDocSpider and DigiDocMetaEdit, designed with the aim of verifYing, evaluating, and promoting its implementation.

Frame detection over the semantic web

In the past, research in ontology learning from text has mainly focused on entity recognition, taxonomy induction and relation extraction. In this work we approach a challenging research issue: detecting semantic frames from texts and using them to encode web ontologies. We exploit a new generation Natural Language Processing technology for frame detection, and we enrich the frames acquired so far with argument restrictions provided by a super-sense tagger and domain specializations. The results are encoded according to a Linguistic MetaModel, which allows a complete translation of lexical resources and data acquired from text, enabling custom transformations of the enriched frames into modular ontology components.