State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

Automatic analysis and validation of open polymer data

A system to automatically extract, analyse, validate and model polymer data has been produced. This system is called the Polymer Informatics Knowledge System (PIKS). Methods of storing polymer data electronically are examined. The majority of data-formats are only capable of representing an idealised structure of a macromolecule rather than the actual distribution of structures present in the polymer. Polymer markup language (PML) is the only data-format capable of storing this information. A novel extension to the PML language, allowing copolymers produced with a depletion of reactants is introduced. Without the extension only Markov-chains can be produced. An informatics analysis of Unilever data of cleaning efficacy of polymers is performed. A representative macromolecule was produced for each polymer sample. Descriptors were calculated over these and used for machine learning to predict the cleaning efficacy. From these models a monomer was identified which was very strongly correlated with good cleaning performance. The monomer in question cannot be revealed as it is a trade secret. Polymer data from the PoLyInfo database are extracted and converted into XML. A summary of the data available in the PoLyInfo Database is presented. The PIKS tools were used to automatically validate this data for internal consistency, as well as against another data source. The monomers and polymers were analysed for consistency, as well as CML reactions being produced for the polymerisation reactions in the database which were also checked for constancy. The error in the structures was found to be 5.8% for the monomers, 7.3% for the polymers and 2.9% for the reactions. Some of the causes of the discrepancies are presented. The property data from the PoLyInfo database was then used for machine learning. Support Vector Regression (SVR) models of the glass transition temperature were produced both with and without the inclusion of sample characterisation data. Both methods performed similarly, with the model without producing an RMS error of 19.1K (r^2=0.96), while the model with produced an RMS error of 20.1K (r^2=0.96). This means that more sample characterisation data is required than the M_w and M_w/M_n.This work was supported by Unileve

State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

Logische Grundlagen von Datenbanktransformationen für Datenbanken mit komplexen Typen

Database transformations consist of queries and updates which are two fundamental types of computations in any databases - the first provides the capability to retrieve data and the second is used to maintain databases in light of ever-changing application domains. With the rising popularity of web-based applications and service-oriented architectures, the development of database transformations must address new challenges, which frequently call for establishing a theoretical framework that unifies both queries and updates over complex-value databases. This dissertation aims to lay down the foundations for establishing a theoretical framework of database transformations in the context of complex-value databases. We shall use an approach that has successfully been used for the characterisation of sequential algorithms. The sequential Abstract State Machine (ASM) thesis captures semantics and behaviour of sequential algorithms. The thesis uses the similarity of general computations and database transformations for characterisation of the later by five postulates: sequential time postulate, abstract state postulate, bounded exploration postulate, background postulate, and the bounded non-determinism postulate. The last two postulates reflect the specific form of transformations for databases. The five postulates exactly capture database transformations. Furthermore, we provide a logical proof system for database transformations that is sound and complete.Datenbanktransformationen sind Anfragen an ein Datenbanksystem oder Modifikationen der Daten des Datenbanksystemes. Diese beiden grundlegenden Arten von Berechnungen auf Datenbanksystemen erlauben zum einem den Zugriff auf Daten und zum anderen die Pflege der Datenbank. Eine theoretische Fundierung von Datenbanktransformationen muss so flexibel sein, dass auch neue web-basierten Anwendungen und den neuen serviceorientierte Architekturen reflektiert sind, sowie auch die komplexeren Datenstrukturen. Diese Dissertation legt die Grundlagen für eine Theoriefundierung durch Datenbanktransformationen, die auch komplexe Datenstrukturen unterstützen. Wir greifen dabei auf einen Zugang zurück, der eine Theorie der sequentiellen Algorithmen bietet. Die sequentielle ASM-These (abstrakte Zustandsmaschinen) beschreibt die Semantik und das Verhalten sequentieller Algorithmen. Die Dissertation nutzt dabei die Gleichartigkeit von allgemeinen Berechnungen und Datenbanktransformationen zur Charakterisierung durch fünf Postulate bzw. Axiome: das Axiom der sequentiellen Ausführung, das Axiom einer abstrakten Charakterisierbarkeit von Zuständen, das Axiom der Begrenzbarkeit von Zustandsänderungen und Zustandssicht, das Axiom der Strukturierung von Datenbanken und das Axiom der Begrenzbarkeit des Nichtdeterminismus. Die letzten beiden Axiome reflektieren die spezifische Seite der Datenbankberechnungen. Die fünf Axiome beschreiben vollständig das Verhalten von Datenbanktransformationen. Weiterhin wird eine Beweiskalkül für Datenbanktransformationen entwickelt, der vollständig und korrekt ist

Alternating register automata on finite words and trees

We study alternating register automata on data words and data trees in relation to logics. A data word (resp. data tree) is a word (resp. tree) whose every position carries a label from a finite alphabet and a data value from an infinite domain. We investigate one-way automata with alternating control over data words or trees, with one register for storing data and comparing them for equality. This is a continuation of the study started by Demri, Lazic and Jurdzinski. From the standpoint of register automata models, this work aims at two objectives: (1) simplifying the existent decidability proofs for the emptiness problem for alternating register automata; and (2) exhibiting decidable extensions for these models. From the logical perspective, we show that (a) in the case of data words, satisfiability of LTL with one register and quantification over data values is decidable; and (b) the satisfiability problem for the so-called forward fragment of XPath on XML documents is decidable, even in the presence of DTDs and even of key constraints. The decidability is obtained through a reduction to the automata model introduced. This fragment contains the child, descendant, next-sibling and following-sibling axes, as well as data equality and inequality tests

Ontology based data integration in life sciences

El objetivo de la tesis es el desarrollo de una solución práctica y estándar para la integración semántica de los datos y servicios biológicos. La tesis estudia escenarios diferentes en los cuales las ontologías pueden beneficiar el desarrollo de los servicios web, su búsqueda y su visibilidad. A pesar de que las ontologías son ampliamente utilizadas en la biología, su uso habitualmente se limita a la definición de las jerarquías taxonómicas. La tesis examina la utilidad de las ontologías para la integración de los datos en el desarrollo de los servicios web semánticos. Las ontologías que definen los tipos de datos biológicos tienen un gran valor para la integración de los datos, especialmente ante un cambio continuo de los estándares. La tesis evalúa la ontología BioMoby para la generación de los servicios web conforme con las especificaciones WS-I y los servicios REST. Otro aspecto muy importante de la tesis es el uso de las ontologías para la descripción de los servicios web. La tesis evalúa la ontología WSDL promovida por el consorcio W3C para la descripción de los servicios y su búsqueda. Finalmente, se considera la integración con las plataformas modernas de la ejecución de los flujos de trabajo como Taverna y Galaxy. A pesar de la creciente popularidad del formato JSON, los servicios web dependen mucho del XML. La herramienta OWL2XS facilita el desarrollo de los servicios web semánticos generando un esquema XML a partir de una ontología OWL 2. La integración de los servicios web es difícil de conseguir sin una adaptación de los estándares. La aplicación BioNemus genera de manera automática servicios web estándar a partir de las ontologías BioMoby. La representación semántica de los servicios web simplifica su búsqueda y anotación. El Registro Semántico de Servicios Web (BioSWR) está basado en la ontología WSDL del W3C y proporciona una representación en distintos formatos: OWL 2, WSDL 1.1, WSDL 2.0 y WADL. Para demostrar los beneficios de la descripción semántica de los servicios web se ha desarrollado un plugin para Taverna. También se ha implementado una nueva librería experimental que ha sido usada en la aplicación Galaxy Gears, la cual permite la integración de los servicios web en Galaxy. La tesis explora el alcance de la aplicación de las ontologías para la integración de los datos y los servicios biológicos, proporcionando un amplio conjunto de nuevas aplicaciones.The aim of this thesis is to develop standard and practical approaches for the semantic integration of biological data and services. The thesis considers various scenarios where ontologies may benefit bioinformatics web services development, integration and provenance. In spite of the broad use of ontologies in biology, their usage is usually limited to a definition of taxonomic hierarchies. This thesis examines the utility of ontologies for data integration in context of semantic web services development. The biological datatypes ontologies are very valuable for the data integration, especially in a context of continuous standards changes. The thesis evaluates the outdated BioMoby ontology for the generation of modern WS-I and RESTful web services. Another important aspect is the use of ontologies for the web services description. The thesis evaluates the W3C standard WSDL ontology for bioinformatics web services description and provenance. Finally, the integration with modern workflow execution platforms such as Taverna and Galaxy is also considered. Despite the growing popularity of JSON format, web services vastly depend on XML type system. The OWL2XS tool facilitates semantic web services development providing the automatic XML Schema generation from an appropriate OWL 2 datatype ontology. Web services integration is hardly achievable without a broad standard adoption. The BioNemus application automatically generates standard-based web services from BioMoby ontologies. Semantic representation of web services description simplifies web services search and annotation. Semantic Web Services Registry (BioSWR) is based on W3C WSDL ontology and provides a multifaceted web services view in different formats: OWL 2, WSDL 1.1, WSDL 2.0 and WADL. To demonstrate benefits of ontology-based web services descriptions, BioSWR Taverna OSGI plug-in has been developed. The new, experimental, Taverna WSDL generic library has been used in Galaxy Gears tool which allows integrating web services into the Galaxy workflows. The thesis explores the scopes of ontologies application for the biological data and services integration, providing a broad set of original tools

Hyperset Approach to Semi-structured Databases and the Experimental Implementation of the Query Language Delta

This thesis presents practical suggestions towards the implementation of the hyperset approach to semi-structured databases and the associated query language Delta. This work can be characterised as part of a top-down approach to semi-structured databases, from theory to practice. The main original part of this work consisted in implementation of the hyperset Delta query language to semi-structured databases, including worked example queries. In fact, the goal was to demonstrate the practical details of this approach and language. The required development of an extended, practical version of the language based on the existing theoretical version, and the corresponding operational semantics. Here we present detailed description of the most essential steps of the implementation. Another crucial problem for this approach was to demonstrate how to deal in reality with the concept of the equality relation between (hyper)sets, which is computationally realised by the bisimulation relation. In fact, this expensive procedure, especially in the case of distributed semi-structured data, required some additional theoretical considerations and practical suggestions for efficient implementation. To this end the 'local/global' strategy for computing the bisimulation relation over distributed semi-structured data was developed and its efficiency was experimentally confirmed.Comment: Technical Report (PhD thesis), University of Liverpool, Englan

A Semantic Web approach to ontology-based system: integrating, sharing and analysing IoT health and fitness data

With the rapid development of fitness industry, Internet of Things (IoT) technology is becoming one of the most popular trends for the health and fitness areas. IoT technologies have revolutionised the fitness and the sport industry by giving users the ability to monitor their health status and keep track of their training sessions. More and more sophisticated wearable devices, fitness trackers, smart watches and health mobile applications will appear in the near future. These systems do collect data non-stop from sensors and upload them to the Cloud. However, from a data-centric perspective the landscape of IoT fitness devices and wellness appliances is characterised by a plethora of representation and serialisation formats. The high heterogeneity of IoT data representations and the lack of common accepted standards, keep data isolated within each single system, preventing users and health professionals from having an integrated view of the various information collected. Moreover, in order to fully exploit the potential of the large amounts of data, it is also necessary to enable advanced analytics over it, thus achieving actionable knowledge. Therefore, due the above situation, the aim of this thesis project is to design and implement an ontology based system to (1) allow data interoperability among heterogeneous IoT fitness and wellness devices, (2) facilitate the integration and the sharing of information and (3) enable advanced analytics over the collected data (Cognitive Computing). The novelty of the proposed solution lies in exploiting Semantic Web technologies to formally describe the meaning of the data collected by the IoT devices and define a common communication strategy for information representation and exchange