A UML profile for the OBO relation ontology

Background: Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results: We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions: The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.

Oral health-related quality of life of paediatric patients with AIDS

Abstract Background Children with Acquired Immune Deficiency Syndrome (AIDS) exhibit impaired dental status, which can affect their quality of life. This study assessed the oral health-related quality of life of these patients and associated factors. Methods The "Child Perceptions Questionnaire 11-14", rating overall and domain-specific (oral symptoms, functional limitations, emotional well being, and social well being) oral health-related quality of life (OHR-QoL) was completed by 88 children with AIDS assisted in the Child Institute, Sao Paulo, Brazil. Parents or guardians provided behavioural and socio-demographic information. The clinical status was provided by hospital records. OHR-QoL covariates were assessed by Poisson regression analysis. Results The most affected OHR-QoL subscale concerned oral symptoms, whose rate was 23.9%. The direct answer for oral health and well being made up a rate of 47.7%. Brushing the teeth less than two times a day and viral load exceeding 10,000 HIV-RNA copies per millilitre of plasma were directly associated (p < 0.05) with a poorer oral health-related quality of life. Conclusions Children with more severe AIDS manifestations complained of poorer status of oral symptoms, functional limitations, emotional and social well being related to their oral health. Recognizing the factors that are associated with poorer OHR-QoL in children with AIDS may contribute to the planning of dental services for this population.

Architectures for Context Aware Services in Smart Environments

This thesis deals with Context Aware Services, Smart Environments, Context Management and solutions for Devices and Service Interoperability. Multi-vendor devices offer an increasing number of services and end-user applications that base their value on the ability to exploit the information originating from the surrounding environment by means of an increasing number of embedded sensors, e.g. GPS, compass, RFID readers, cameras and so on. However, usually such devices are not able to exchange information because of the lack of a shared data storage and common information exchange methods. A large number of standards and domain specific building blocks are available and are heavily used in today's products. However, the use of these solutions based on ready-to-use modules is not without problems. The integration and cooperation of different kinds of modules can be daunting because of growing complexity and dependency. In this scenarios it might be interesting to have an infrastructure that makes the coexistence of multi-vendor devices easy, while enabling low cost development and smooth access to services. This sort of technologies glue should reduce both software and hardware integration costs by removing the trouble of interoperability. The result should also lead to faster and simplified design, development and, deployment of cross-domain applications. This thesis is mainly focused on SW architectures supporting context aware service providers especially on the following subjects: - user preferences service adaptation - context management - content management - information interoperability - multivendor device interoperability - communication and connectivity interoperability Experimental activities were carried out in several domains including Cultural Heritage, indoor and personal smart spaces – all of which are considered significant test-beds in Context Aware Computing. The work evolved within european and national projects: on the europen side, I carried out my research activity within EPOCH, the FP6 Network of Excellence on “Processing Open Cultural Heritage” and within SOFIA, a project of the ARTEMIS JU on embedded systems. I worked in cooperation with several international establishments, including the University of Kent, VTT (the Technical Reserarch Center of Finland) and Eurotech. On the national side I contributed to a one-to-one research contract between ARCES and Telecom Italia. The first part of the thesis is focused on problem statement and related work and addresses interoperability issues and related architecture components. The second part is focused on specific architectures and frameworks: - MobiComp: a context management framework that I used in cultural heritage applications - CAB: a context, preference and profile based application broker which I designed within EPOCH Network of Excellence - M3: "Semantic Web based" information sharing infrastructure for smart spaces designed by Nokia within the European project SOFIA - NoTa: a service and transport independent connectivity framework - OSGi: the well known Java based service support framework The final section is dedicated to the middleware, the tools and, the SW agents developed during my Doctorate time to support context-aware services in smart environments.

Frame-driven Extraction of Linked Data and Ontologies from Text

Ontology design and population -core aspects of semantic technologies- re- cently have become fields of great interest due to the increasing need of domain-specific knowledge bases that can boost the use of Semantic Web. For building such knowledge resources, the state of the art tools for ontology design require a lot of human work. Producing meaningful schemas and populating them with domain-specific data is in fact a very difficult and time-consuming task. Even more if the task consists in modelling knowledge at a web scale. The primary aim of this work is to investigate a novel and flexible method- ology for automatically learning ontology from textual data, lightening the human workload required for conceptualizing domain-specific knowledge and populating an extracted schema with real data, speeding up the whole ontology production process. Here computational linguistics plays a fundamental role, from automati- cally identifying facts from natural language and extracting frame of relations among recognized entities, to producing linked data with which extending existing knowledge bases or creating new ones. In the state of the art, automatic ontology learning systems are mainly based on plain-pipelined linguistics classifiers performing tasks such as Named Entity recognition, Entity resolution, Taxonomy and Relation extraction [11]. These approaches present some weaknesses, specially in capturing struc- tures through which the meaning of complex concepts is expressed [24]. Humans, in fact, tend to organize knowledge in well-defined patterns, which include participant entities and meaningful relations linking entities with each other. In literature, these structures have been called Semantic Frames by Fill- 6 Introduction more [20], or more recently as Knowledge Patterns [23]. Some NLP studies has recently shown the possibility of performing more accurate deep parsing with the ability of logically understanding the structure of discourse [7]. In this work, some of these technologies have been investigated and em- ployed to produce accurate ontology schemas. The long-term goal is to collect large amounts of semantically structured information from the web of crowds, through an automated process, in order to identify and investigate the cognitive patterns used by human to organize their knowledge.

Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Contaminazioni tra arte e architettura

Il concetto di contaminazione fra architettura ed arti plastiche e figurative è molto antico. La dicotomia arte-architettura, sancita in via definitiva con il moderno museo di spoliazione napoleonica, non può che essere considerata una variazione neo-tecnicista sulla quale, non sempre giustamente, sono andati assestandosi gli insegnamenti delle scuole politecniche. Non così è sempre stato. Come il tempio greco può essere considerato un’opera plastica nel suo complesso, esempio tra i primi di fusione tra arte e architettura, moltissimi sono gli esempi che hanno guidato la direzione della ricerca che si è intesa perseguire. Molti sono gli esempi del passato che ci presentano figure di architetto-artista: un esempio fra tutti Michelangelo Buonarroti; come per altro non è nuovo, per l’artista puro, cimentarsi nella progettazione dello spazio architettonico o urbano, o per l'architetto essere coinvolto dalle indagini della ricerca artistica a lui contemporanea dalla quale trarre suggestioni culturali. Le rappresentazioni dei linguaggi visivi sono il frutto di contaminazioni che avvengono su diversi livelli e in più direzioni. Spesso le ricerche artistiche più significative hanno anticipato o influenzato il mondo del design, dell’architettura, della comunicazione. L’intenzione della ricerca è stata quindi approfondire, attraverso un viaggio nel Novecento, con particolare attenzione al Secondo Dopoguerra, i fenomeni culturali che hanno prodotto i più significativi sviluppi stilistici nell’ambito della ricerca e del rinnovo del linguaggio architettonico. Il compito, parafrasando Leonardo Benevolo, non è stato quello di elencare le singole battute della discussione ma di riconoscere gli interventi fruttuosi a lunga scadenza. Mutuando gli insegnamenti della scuola del Bauhaus, arte e architettura sono state affiancate perché considerate espressioni strettamente relazionate di coevi fenomeni culturali. L’obiettivo ha puntato all’individuazione dei meccanismi delle interazioni tra discipline, cercando di delineare il profilo della complessità dell’espressione del contemporaneo in architettura.

Spagnolo Tecnico Semplificato

L’obiettivo della presente dissertazione è quello di creare un nuovo linguaggio controllato, denominato Español Técnico Simplificado (ETS). Basato sulla specifica tecnica del Simplified Technical English (STE), ufficialmente conosciuta come ASD-STE100, lo spagnolo controllato ETS si presenta come un documento metalinguistico in grado di fornire ad un redattore o traduttore tecnico alcune regole specifiche per produrre un documento tecnico. La strategia di implementazione conduce allo studio preliminare di alcuni linguaggi controllati simili all’inglese STE, quali il Français Rationalisé e il Simplified Technical Spanish. Attraverso un approccio caratteristico della linguistica dei corpora, la soluzione proposta fornisce il nuovo linguaggio controllato mediante l’estrazione di informazioni specifiche da un corpus ad-hoc di lingua spagnola appositamente creato ed interrogato. I risultati evidenziano un metodo linguistico (controllato) utile a produrre documentazione tecnica priva di ogni eventuale ambiguità. Il sistema ETS, infatti, si fonda sul concetto della intelligibilità in quanto condizione necessaria da soddisfare nell’ambito della produzione di un testo controllato. E, attraverso la sua macrostruttura, il documento ETS fornisce gli strumenti necessari per rendere il testo controllato univoco. Infatti, tale struttura bipartita suddivide in maniera logica i dettami: una prima parte riguarda e contiene regole sintattiche e stilistiche; una seconda parte riguarda e contiene un dizionario di un numero limitato di lemmi opportunamente selezionati. Il tutto a favore del principio della biunivocità dei segni, in questo caso, della lingua spagnola. Il progetto, nel suo insieme, apre le porte ad un linguaggio nuovo in alternativa a quelli presenti, totalmente creato in accademia, che vale come prototipo a cui far seguire altri progetti di ricerca.

Una scossa all'economia: le conseguenze del sisma dell'Aquilano. Traduzione dall'inglese in italiano di un articolo di ricerca economica ed esperienza di collaborazione con gli autori.

The aim of this dissertation is to provide a translation from English into Italian of a specialised scientific article published in the Cambridge Working Papers in Economics series. In this text, the authors estimate the economic consequences of the earthquake that hit the Abruzzo region in 2009. An extract of this translation will be published as part of conference proceedings. The main reason behind this choice is a personal interest in specialised translation in the economic domain. Moreover, the subject of the article is of particular interest to the Italian readership. The aim of this study is to show how a non-specialised translator can tackle with such a highly specialised translation with the use of appropriate terminology resources and the collaboration of field experts. The translation could be of help to other Italian linguists looking for translated material in this particular domain where English seems to be the dominant language. In order to ensure consistent terminology and adequate style, the document has been translated with the use of different resources, such as dictionaries, glossaries and specialised corpora. I also contacted field experts and the authors of text. The collaboration with the authors proved to be an invaluable resource yet one to be carefully managed. This work is divided into 5 chapters. The first deals with domain-specific sublanguages. The second gives an overview of corpus linguistics and describes the corpora designed for the translation. The third provides an analysis of the article, focusing on syntactical, lexical and structural features while the fourth presents the translation, side-by-side with the source text. The fifth comments on the main difficulties encountered in the translation and the strategies used, as well as the relationship with the authors and their review of the published text. Appendix I contains the econometric glossary English – Italian.

Imagery of a moving object: the role of occipital cortex and human MT/V5+

Visual imagery – similar to visual perception – activates feature-specific and category-specific visual areas. This is frequently observed in experiments where the instruction is to imagine stimuli that have been shown immediately before the imagery task. Hence, feature-specific activation could be related to the short-term memory retrieval of previously presented sensory information. Here, we investigated mental imagery of stimuli that subjects had not seen before, eliminating the effects of short-term memory. We recorded brain activation using fMRI while subjects performed a behaviourally controlled guided imagery task in predefined retinotopic coordinates to optimize sensitivity in early visual areas. Whole brain analyses revealed activation in a parieto-frontal network and lateral–occipital cortex. Region of interest (ROI) based analyses showed activation in left hMT/V5+. Granger causality mapping taking left hMT/V5+ as source revealed an imagery-specific directed influence from the left inferior parietal lobule (IPL). Interestingly, we observed a negative BOLD response in V1–3 during imagery, modulated by the retinotopic location of the imagined motion trace. Our results indicate that rule-based motion imagery can activate higher-order visual areas involved in motion perception, with a role for top-down directed influences originating in IPL. Lower-order visual areas (V1, V2 and V3) were down-regulated during this type of imagery, possibly reflecting inhibition to avoid visual input from interfering with the imagery construction. This suggests that the activation in early visual areas observed in previous studies might be related to short- or long-term memory retrieval of specific sensory experiences.

Domains of physical activity and all-cause mortality: systematic review and dose-response meta-analysis of cohort studies

Background The dose–response relation between physical activity and all-cause mortality is not well defined at present. We conducted a systematic review and meta-analysis to determine the association with all-cause mortality of different domains of physical activity and of defined increases in physical activity and energy expenditure. Methods MEDLINE, Embase and the Cochrane Library were searched up to September 2010 for cohort studies examining all-cause mortality across different domains and levels of physical activity in adult general populations. We estimated combined risk ratios (RRs) associated with defined increments and recommended levels, using random-effects meta-analysis and dose–response meta-regression models. Results Data from 80 studies with 1 338 143 participants (118 121 deaths) were included. Combined RRs comparing highest with lowest activity levels were 0.65 [95% confidence interval (95% CI) 0.60–0.71] for total activity, 0.74 (95% CI 0.70–0.77) for leisure activity, 0.64 (95% CI 0.55–0.75) for activities of daily living and 0.83 (95% CI 0.71–0.97) for occupational activity. RRs per 1-h increment per week were 0.91 (95% CI 0.87–0.94) for vigorous exercise and 0.96 (95% CI 0.93–0.98) for moderate-intensity activities of daily living. RRs corresponding to 150 and 300 min/week of moderate to vigorous activity were 0.86 (95% CI 0.80–0.92) and 0.74 (95% CI 0.65–0.85), respectively. Mortality reductions were more pronounced in women. Conclusion Higher levels of total and domain-specific physical activity were associated with reduced all-cause mortality. Risk reduction per unit of time increase was largest for vigorous exercise. Moderate-intensity activities of daily living were to a lesser extent beneficial in reducing mortality.

Extracting models from IDEs

Systems must co-evolve with their context. Reverse engineering tools are a great help in this process of required adaption. In order for these tools to be flexible, they work with models, abstract representations of the source code. The extraction of such information from source code can be done using a parser. However, it is fairly tedious to build new parsers. And this is made worse by the fact that it has to be done over and over again for every language we want to analyze. In this paper we propose a novel approach which minimizes the knowledge required of a certain language for the extraction of models implemented in that language by reflecting on the implementation of preparsed ASTs provided by an IDE. In a second phase we use a technique referred to as Model Mapping by Example to map platform dependent models onto domain specific model.

Kostenorientiertes Controlling von E-Learning-Plattformen mit dem TCO-Konzept

Zur administrativen Unterstützung von Lehr- und Lernprozessen werden E-Learning-Plattformen eingesetzt, die auf der Grundlage des Internet Funktionen zur Distribution von Lehr- und Lernmaterialien und zur Kommunikation zwischen Lehrenden und Lernenden anbieten. Zahlreiche wissenschaftliche Beiträge und Marktstudien beschäftigen sich mit der multikriteriellen Evaluation dieser Softwareprodukte zur informatorischen Fundierung strategischer Investitionsentscheidungen. Demgegenüber werden Instrumente zum kostenorientierten Controlling von E-Learning-Plattformen allenfalls marginal thematisiert. Dieser Beitrag greift daher das Konzept der Total Cost of Ownership (TCO) auf, das einen methodischen Ansatzpunkt zur Schaffung von Kostentransparenz von E-Learning-Plattformen bildet. Aufbauend auf den konzeptionellen Grundlagen werden Problembereiche und Anwendungspotenziale für das kostenorientierte Controlling von LMS identifiziert. Zur softwaregestützten Konstruktion und Analyse von TCO-Modellen wird das Open Source-Werkzeug TCO-Tool eingeführt und seine Anwendung anhand eines synthetischen Fallbeispiels erörtert. Abschließend erfolgt die Identifikation weiterführender Entwicklungsperspektiven des TCO-Konzepts im Kontext des E-Learning. Die dargestellte Thematik ist nicht nur von theoretischem Interesse, sondern adressiert auch den steigenden Bedarf von Akteuren aus der Bildungspraxis nach Instrumenten zur informatorischen Fundierung von Investitions- und Desinvestitionsentscheidungen im Umfeld des E-Learning.

Health related quality of life: a changing construct?

In 186 patients with early colon cancer, we investigated the assumption that the meaning of 'quality of life' (QL) remains constant over time. Within a phase-III trial (SAKK 40/93), patients estimated both their overall QL and a range of disease- and treatment-related domains at five timepoints, comprising three concurrent and 2 retrospective estimates: their pre-surgery QL both before surgery and retrospectively thereafter, and their pre-adjuvant QL both at the beginning of adjuvant treatment and retrospectively about 2 months later, and their current QL 2 weeks thereafter. Multilevel models were developed to determine whether the selected domains made stable contributions to overall QL at the concurrent estimates. The weights of the domains changed over time. They did not differ significantly according to whether patients were considering their concurrent state or reflecting on this state at a later timepoint. In the process of adaptation, patients with early colon cancer substantially change the relative importance of QL domains to overall QL. This finding argues for QL as a changing construct and against the assumption that domain-specific weights are stable across distinct clinical phases.

Do implicit motives and basic psychological needs interact to predict well-being and flow? Testing a universal hypothesis and a matching hypothesis

Self-Determination Theory (Deci and Ryan in Intrinsic motivation and self-determination in human behavior. Plenum Press, New York, 1985) suggests that certain experiences, such as competence, are equally beneficial to everyone’s well-being (universal hypothesis), whereas Motive Disposition Theory (McClelland in Human motivation. Scott, Foresman, Glenview, IL, 1985) predicts that some people, such as those with a high achievement motive, should benefit particularly from such experiences (matching hypothesis). Existing research on motives as moderators of the relationship between basic need satisfaction and positive outcomes supports both these seemingly inconsistent views. Focusing on the achievement motive, we sought to resolve this inconsistency by considering the specificity of the outcome variables. When predicting domain-specific well-being and flow, the achievement motive should interact with felt competence. However, when it comes to predicting general well-being and flow, felt competence should unfold its effects without being moderated by the achievement motive. Two studies confirmed these assumptions indicating that the universal and matching hypotheses are complementary rather than mutually exclusive.