The TOG Conclusions Background

Information overload, (non-)interoperability of software tool

Spatio-structural granularity of biological material entities

<p>Abstract</p> <p>Background</p> <p>With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.</p> <p>Results</p> <p>The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the <it>compositional object perspective </it>as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities.</p> <p>Conclusions</p> <p>The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different <it>views </it>on its content (i.e. data, knowledge), each organized into different levels of detail.</p

Decentralized Control and Adaptation in Distributed Applications via Web and Semantic Web Technologies

The presented work provides an approach and an implementation for enabling decentralized control in distributed applications composed of heterogeneous components by benefiting from the interoperability provided by the Web stack and relying on semantic technologies for enabling data integration. In particular, the concept of Smart Components enables adaptability at runtime through an adaptation layer and is complemented by a reference architecture as well as a prototypical implementation

Inferring Complex Activities for Context-aware Systems within Smart Environments

The rising ageing population worldwide and the prevalence of age-related conditions such as physical fragility, mental impairments and chronic diseases have significantly impacted the quality of life and caused a shortage of health and care services. Over-stretched healthcare providers are leading to a paradigm shift in public healthcare provisioning. Thus, Ambient Assisted Living (AAL) using Smart Homes (SH) technologies has been rigorously investigated to help address the aforementioned problems. Human Activity Recognition (HAR) is a critical component in AAL systems which enables applications such as just-in-time assistance, behaviour analysis, anomalies detection and emergency notifications. This thesis is aimed at investigating challenges faced in accurately recognising Activities of Daily Living (ADLs) performed by single or multiple inhabitants within smart environments. Specifically, this thesis explores five complementary research challenges in HAR. The first study contributes to knowledge by developing a semantic-enabled data segmentation approach with user-preferences. The second study takes the segmented set of sensor data to investigate and recognise human ADLs at multi-granular action level; coarse- and fine-grained action level. At the coarse-grained actions level, semantic relationships between the sensor, object and ADLs are deduced, whereas, at fine-grained action level, object usage at the satisfactory threshold with the evidence fused from multimodal sensor data is leveraged to verify the intended actions. Moreover, due to imprecise/vague interpretations of multimodal sensors and data fusion challenges, fuzzy set theory and fuzzy web ontology language (fuzzy-OWL) are leveraged. The third study focuses on incorporating uncertainties caused in HAR due to factors such as technological failure, object malfunction, and human errors. Hence, existing studies uncertainty theories and approaches are analysed and based on the findings, probabilistic ontology (PR-OWL) based HAR approach is proposed. The fourth study extends the first three studies to distinguish activities conducted by more than one inhabitant in a shared smart environment with the use of discriminative sensor-based techniques and time-series pattern analysis. The final study investigates in a suitable system architecture with a real-time smart environment tailored to AAL system and proposes microservices architecture with sensor-based off-the-shelf and bespoke sensing methods. The initial semantic-enabled data segmentation study was evaluated with 100% and 97.8% accuracy to segment sensor events under single and mixed activities scenarios. However, the average classification time taken to segment each sensor events have suffered from 3971ms and 62183ms for single and mixed activities scenarios, respectively. The second study to detect fine-grained-level user actions was evaluated with 30 and 153 fuzzy rules to detect two fine-grained movements with a pre-collected dataset from the real-time smart environment. The result of the second study indicate good average accuracy of 83.33% and 100% but with the high average duration of 24648ms and 105318ms, and posing further challenges for the scalability of fusion rule creations. The third study was evaluated by incorporating PR-OWL ontology with ADL ontologies and Semantic-Sensor-Network (SSN) ontology to define four types of uncertainties presented in the kitchen-based activity. The fourth study illustrated a case study to extended single-user AR to multi-user AR by combining RFID tags and fingerprint sensors discriminative sensors to identify and associate user actions with the aid of time-series analysis. The last study responds to the computations and performance requirements for the four studies by analysing and proposing microservices-based system architecture for AAL system. A future research investigation towards adopting fog/edge computing paradigms from cloud computing is discussed for higher availability, reduced network traffic/energy, cost, and creating a decentralised system. As a result of the five studies, this thesis develops a knowledge-driven framework to estimate and recognise multi-user activities at fine-grained level user actions. This framework integrates three complementary ontologies to conceptualise factual, fuzzy and uncertainties in the environment/ADLs, time-series analysis and discriminative sensing environment. Moreover, a distributed software architecture, multimodal sensor-based hardware prototypes, and other supportive utility tools such as simulator and synthetic ADL data generator for the experimentation were developed to support the evaluation of the proposed approaches. The distributed system is platform-independent and currently supported by an Android mobile application and web-browser based client interfaces for retrieving information such as live sensor events and HAR results

An Ontology-Driven Sociomedical Web 3.0 Framework

Web 3.0, the web of social and semantic cooperation, calls for a methodological multidisciplinary architecture in order to reach its mainstream objectives. With the lack of such an architecture and the reliance of existing efforts on lightweight semantics and RDF graphs, this thesis proposes "Web3.OWL", an ontology-driven framework towards a Web 3.0 knowledge architecture. Meanwhile, the online social parenting data and their corresponding websites users known as "mommy bloggers" undergo one of the fastest online demographics growth, and the available literature reflects the very little attention this growth has so far been given and the various deficiencies the parenting domain suffers from; these deficiencies all fall under the umbrella of the scarcity of parenting sociomedical analysis and decision-support systems. The Web3.OWL framework puts forward an approach that relies on the Meta-Object Facility for Semantics standard (SMOF) for the management of its modeled OWL (Web Ontology Language) expressive domain ontologies on the one hand, and the coordination of its various underlined Web 3.0 prerequisite disciplines on the other. Setting off with a holistic portrayal of Web3.OWL’s components and workflow, the thesis progresses into a more analytic exploration of its main paradigms. Out of its different ontology-aware paradigms are notably highlighted both its methodology for expressiveness handling through modularization and projection techniques and algorithms, and its facilities for tagging inference, suggestion and processing. Web3.OWL, albeit generic by conception, proves its efficiency in solving the deficiencies and meeting the requirements of the sociomedical domain of interest. Its conceived ontology for parenting analysis and surveillance, baptised "ParOnt", strongly contributes to the backbone metamodel and the various constituents of this ontology-driven framework. Accordingly, as the workflow revolves around Description Logics principles, OWL 2 profiles along with standard and beyond-standard reasoning techniques, conducted experiments and competency questions are illustrated, thus establishing the required Web 3.0 outcomes. The empirical results of the diverse preliminary decision-support and recommendation services targeting parenting public awareness, orientation and education do ascertain, in conclusion, the value and potentials of the proposed conceptual framework

Using ontology and semantic web services to support modeling in systems biology

This thesis addresses the problem of collaboration among experimental biologists and modelers in the study of systems biology by using ontology and Semantic Web Services techniques. Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models across different biological scales. This requires interoperation among various knowledge sources and services. Ontology and Semantic Web Services potentially provide an infrastructure to meet this requirement. In our study, we propose an ontology-centered framework within the Semantic Web infrastructure that aims at standardizing various areas of knowledge involved in the biological modeling processes. In this framework, first we specify an ontology-based meta-model for building biological models. This meta-model supports using shared biological ontologies to annotate biological entities in the models, allows semantic queries and automatic discoveries, enables easy model reuse and composition, and serves as a basis to embed external knowledge. We also develop means of transforming biological data sources and data analysis methods into Web Services. These Web Services can then be composed together to perform parameterization in biological modeling. The knowledge of decision-making and workflow of parameterization processes are then recorded by the semantic descriptions of these Web Services, and embedded in model instances built on our proposed meta-model. We use three cases of biological modeling to evaluate our framework. By examining our ontology-centered framework in practice, we conclude that by using ontology to represent biological models and using Semantic Web Services to standardize knowledge components in modeling processes, greater capabilities of knowledge sharing, reuse and collaboration can be achieved. We also conclude that ontology-based biological models with formal semantics are essential to standardize knowledge in compliance with the Semantic Web vision

Conectando dados biológicos : dos fenótipos às árvores filogenéticas

Orientador: André SantanchèDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Um grande número de estudos em biologia, incluindo os que envolvem a reconstrução de árvores filogenéticas, resultam na produção de uma enorme quantidade de dados -- por exemplo, descrições fenotípicas , matrizes de dados morfológicos , árvores filogenéticas, etc. Biólogos enfrentam cada vez mais o desafio e a oportunidade de efetivamente descobrir conhecimento a partir do cruzamento e comparação de vários conjuntos de dados, nem sempre conectados e integrados. Neste trabalho, estamos interessados em um contexto específico da biologia em que biólogos aplicam ferramentas computacionais para construir e compartilhar descrições digitais dos seres vivos. Nós propomos um processo que parte de fontes de dados fragmentadas, que nós mapeamos para grafos, em direção a uma plena integração das descrições através de ontologias. Os bancos de dados de grafos intermediam o processo de evolução. Eles são menos dependentes de esquema e, uma vez que ontologias também são grafos, o processo de mapeamento do grafo inicial para uma ontologia torna-se uma sequência de transformações no grafo. Nossa motivação parte da ideia de que a conversão de descrições fenotípicas em uma rede de relações e a busca de conexões entre elementos relacionados irá aumentar a capacidade de resolver problemas mais complexos suportados por computadores. Este trabalho detalha os princípios de concepção por trás do nosso processo e duas implementações práticas como prova de conceitoAbstract: A large number of studies in biology, including those involving phylogenetic trees reconstruction, result in the production of a huge amount of data -- e.g., phenotype descriptions, morphological data matrices, phylogenetic trees, etc. Biologists increasingly face a challenge and opportunity of effectively discovering useful knowledge crossing and comparing several pieces of information, not always linked and integrated. In this work, we are interested in a specific biology context, in which biologists apply computational tools to build and share digital descriptions of living beings. We propose a process that departs from fragmentary data sources, which we map to graphs, towards a full integration of descriptions through ontologies. Graph databases mediate this evolvement process. They are less schema dependent and, since an ontology is also a graph, the mapping process from the initial graph towards an ontology becomes a sequence of graph transformations. Our motivation stems from the idea that transforming phenotypical descriptions in a network of relationships and looking for links among related elements will enhance the ability of solving more complex problems supported by machines. This work details the design principles behind our process and two practical implementations as proof of conceptMestradoCiência da ComputaçãoMestre em Ciência da Computaçã