The Blood Ontology: An ontology in the domain of hematology

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some of its anticipated uses

Methodological approaches and techniques for designing ontologies in information systems requirements engineering

Programa doutoral em Information Systems and TechnologyThe way we interact with the world around us is changing as new challenges arise, embracing innovative business models, rethinking the organization and processes to maximize results, and evolving change management. Currently, and considering the projects executed, the methodologies used do not fully respond to the companies' needs. On the one hand, organizations are not familiar with the languages used in Information Systems, and on the other hand, they are often unable to validate requirements or business models. These are some of the difficulties encountered that lead us to think about formulating a new approach. Thus, the state of the art presented in this paper includes a study of the models involved in the software development process, where traditional methods and the rivalry of agile methods are present. In addition, a survey is made about Ontologies and what methods exist to conceive, transform, and represent them. Thus, after analyzing some of the various possibilities currently available, we began the process of evolving a method and developing an approach that would allow us to design ontologies. The method we evolved and adapted will allow us to derive terminologies from a specific domain, aggregating them in order to facilitate the construction of a catalog of terminologies. Next, the definition of an approach to designing ontologies will allow the construction of a domain-specific ontology. This approach allows in the first instance to integrate and store the data from different information systems of a given organization. In a second instance, the rules for mapping and building the ontology database are defined. Finally, a technological architecture is also proposed that will allow the mapping of an ontology through the construction of complex networks, allowing mapping and relating terminologies. This doctoral work encompasses numerous Research & Development (R&D) projects belonging to different domains such as Software Industry, Textile Industry, Robotic Industry and Smart Cities. Finally, a critical and descriptive analysis of the work done is performed, and we also point out perspectives for possible future work.A forma como interagimos com o mundo à nossa volta está a mudar à medida que novos desafios surgem, abraçando modelos empresariais inovadores, repensando a organização e os processos para maximizar os resultados, e evoluindo a gestão da mudança. Atualmente, e considerando os projetos executados, as metodologias utilizadas não respondem na totalidade às necessidades das empresas. Por um lado, as organizações não estão familiarizadas com as linguagens utilizadas nos Sistemas de Informação, por outro lado, são muitas vezes incapazes de validar requisitos ou modelos de negócio. Estas são algumas das dificuldades encontradas que nos levam a pensar na formulação de uma nova abordagem. Assim, o estado da arte apresentado neste documento inclui um estudo dos modelos envolvidos no processo de desenvolvimento de software, onde os métodos tradicionais e a rivalidade de métodos ágeis estão presentes. Além disso, é efetuado um levantamento sobre Ontologias e quais os métodos existentes para as conceber, transformar e representar. Assim, e após analisarmos algumas das várias possibilidades atualmente disponíveis, iniciou-se o processo de evolução de um método e desenvolvimento de uma abordagem que nos permitisse conceber ontologias. O método que evoluímos e adaptamos permitirá derivar terminologias de um domínio específico, agregando-as de forma a facilitar a construção de um catálogo de terminologias. Em seguida, a definição de uma abordagem para conceber ontologias permitirá a construção de uma ontologia de um domínio específico. Esta abordagem permite em primeira instância, integrar e armazenar os dados de diferentes sistemas de informação de uma determinada organização. Num segundo momento, são definidas as regras para o mapeamento e construção da base de dados ontológica. Finalmente, é também proposta uma arquitetura tecnológica que permitirá efetuar o mapeamento de uma ontologia através da construção de redes complexas, permitindo mapear e relacionar terminologias. Este trabalho de doutoramento engloba inúmeros projetos de Investigação & Desenvolvimento (I&D) pertencentes a diferentes domínios como por exemplo Indústria de Software, Indústria Têxtil, Indústria Robótica e Smart Cities. Finalmente, é realizada uma análise critica e descritiva do trabalho realizado, sendo que apontamos ainda perspetivas de possíveis trabalhos futuros

Engineering polymer informatics: Towards the computer-aided design of polymers

The computer-aided design of polymers is one of the holy grails of modern chemical informatics and of significant interest for a number of communities in polymer science. The paper outlines a vision for the in silico design of polymers and presents an information model for polymers based on modern semantic web technologies, thus laying the foundations for achieving the vision

Domain Analysis, Discourse Community and Literary and Semantic Warrants: a study of the Brazilian rural landscape

The current study deals with the theoretical and methodological feasibility of the use of domain analysis and discourse community, by means of literary and semantic warrants, aiming at the identification of the rural landscape in its ontological dimension, having Knowledge Organization Systems (KOS) as a purpose. The rural landscape and its network of concepts within the field of Information Science (IS) are analyzed in relation to geographic knowledge representation and organization. The methodological procedures, subdivided into bibliographical research and documentary research, included the examination of the 1970 and 2006 editions of the Census of Agriculture, under the responsibility of the Brazilian Institute of Geography and Statistics, and of representation of the rural landscapes in bibliographic classification systems, thesauri, and ontologies. Results show conceptual and standardized landscape terminology by means of the conceptualization of the categories that represent it, resulting from the Geography domain and aggregated to information taken from the 1970 and 200 censuses of agriculture.Estudio que presenta la viabilidad teórico-metodológica del uso del análisis de dominio y comunidad discursiva, a través de garantías literaria y semántica, con el fin de conocer e identificar la dimensión ontológica del paisaje rural, objetivando los Sistemas de Organización del Conocimiento (SOCs). Se analiza el paisaje rural y su red de conceptos en el área de las Ciencias de la Información con relación a la organización y representación del conocimiento geográfico. Los procedimientos metodológicos se dividieron en investigación bibliográfica e investigación documental que examinó los Censos Agropecuarios de 1970 y 2006, bajo la responsabilidad del Instituto Brasileño de Geografía y Estadística (IBGE), así como también examinó la representación del paisaje en los sistemas de clasificación bibliográfica, tesauros y ontologías. Como resultado, se obtuvo la terminología conceptual y estandarizada del paisaje a través de la conceptualización de las categorías que lo representan, resultante del dominio de la Geografía y agregadas a las informaciones provenientes de los censos agropecuarios de 1970 y 2006.The current study deals with the theoretical and methodological feasibility of the use of domain analysis and discourse community, by means of literary and semantic warrants, aiming at the identification of the rural landscape in its ontological dimension, having Knowledge Organization Systems (KOS) as a purpose. The rural landscape and its network of concepts within the field of Library and Information Science (LIS) are analyzed in relation to geographic knowledge representation and organization. The methodological procedures, subdivided into bibliographical research and documentary research, included the examination of the 1970 and 2006 editions of the Brazilian Census of Agriculture, under the responsibility of the Brazilian Institute of Geography and Statistics, and of representation of the rural landscapes in bibliographic classification systems, thesauri, and ontologies. Results show conceptual and standardized landscape terminology by means of the conceptualization of the categories that represent it, resulting from the geography domain and aggregated to information taken from the 1970 and 2006 Brazilian censuses of agriculture

LinkedScales : bases de dados em multiescala

Orientador: André SantanchèTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: As ciências biológicas e médicas precisam cada vez mais de abordagens unificadas para a análise de dados, permitindo a exploração da rede de relacionamentos e interações entre elementos. No entanto, dados essenciais estão frequentemente espalhados por um conjunto cada vez maior de fontes com múltiplos níveis de heterogeneidade entre si, tornando a integração cada vez mais complexa. Abordagens de integração existentes geralmente adotam estratégias especializadas e custosas, exigindo a produção de soluções monolíticas para lidar com formatos e esquemas específicos. Para resolver questões de complexidade, essas abordagens adotam soluções pontuais que combinam ferramentas e algoritmos, exigindo adaptações manuais. Abordagens não sistemáticas dificultam a reutilização de tarefas comuns e resultados intermediários, mesmo que esses possam ser úteis em análises futuras. Além disso, é difícil o rastreamento de transformações e demais informações de proveniência, que costumam ser negligenciadas. Este trabalho propõe LinkedScales, um dataspace baseado em múltiplos níveis, projetado para suportar a construção progressiva de visões unificadas de fontes heterogêneas. LinkedScales sistematiza as múltiplas etapas de integração em escalas, partindo de representações brutas (escalas mais baixas), indo gradualmente para estruturas semelhantes a ontologias (escalas mais altas). LinkedScales define um modelo de dados e um processo de integração sistemático e sob demanda, através de transformações em um banco de dados de grafos. Resultados intermediários são encapsulados em escalas reutilizáveis e transformações entre escalas são rastreadas em um grafo de proveniência ortogonal, que conecta objetos entre escalas. Posteriormente, consultas ao dataspace podem considerar objetos nas escalas e o grafo de proveniência ortogonal. Aplicações práticas de LinkedScales são tratadas através de dois estudos de caso, um no domínio da biologia -- abordando um cenário de análise centrada em organismos -- e outro no domínio médico -- com foco em dados de medicina baseada em evidênciasAbstract: Biological and medical sciences increasingly need a unified, network-driven approach for exploring relationships and interactions among data elements. Nevertheless, essential data is frequently scattered across sources with multiple levels of heterogeneity. Existing data integration approaches usually adopt specialized, heavyweight strategies, requiring a costly upfront effort to produce monolithic solutions for handling specific formats and schemas. Furthermore, such ad-hoc strategies hamper the reuse of intermediary integration tasks and outcomes. This work proposes LinkedScales, a multiscale-based dataspace designed to support the progressive construction of a unified view of heterogeneous sources. It departs from raw representations (lower scales) and goes towards ontology-like structures (higher scales). LinkedScales defines a data model and a systematic, gradual integration process via operations over a graph database. Intermediary outcomes are encapsulated as reusable scales, tracking the provenance of inter-scale operations. Later, queries can combine both scale data and orthogonal provenance information. Practical applications of LinkedScales are discussed through two case studies on the biology domain -- addressing an organism-centric analysis scenario -- and the medical domain -- focusing on evidence-based medicine dataDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação141353/2015-5CAPESCNP

Ontology based model framework for conceptual design of treatment flow sheets

The primary objective of wastewater treatment is the removal of pollutants to meet given legal effluent standards. To further reduce operators costs additional recovery of resources and energy is desired by industrial and municipal wastewater treatment. Hence the objective in early stage of planning of treatment facilities lies in the identification and evaluation of promising configurations of treatment units. Obviously this early stage of planning may best be supported by software tools to be able to deal with a variety of different treatment configurations. In chemical process engineering various design tools are available that automatically identify feasible process configurations for the purpose to obtain desired products from given educts. In contrast, the adaptation of these design tools for the automatic generation of treatment unit configurations (process chains) to achieve preset effluent standards is hampered by the following three reasons. First, pollutants in wastewater are usually not defined as chemical substances but by compound parameters according to equal properties (e.g. all particulate matter). Consequently the variation of a single compound parameter leads to a change of related parameters (e.g. relation between Chemical Oxygen Demand and Total Suspended Solids). Furthermore, mathematical process models of treatment processes are tailored towards fractions of compound parameters. This hampers the generic representation of these process models which in turn is essential for automatic identification of treatment configurations. Second, treatment technologies for wastewater treatment rely on a variety of chemical, biological, and physical phenomena. Approaches to mathematically describe these phenomena cover a wide range of modeling techniques including stochastic, conceptual or deterministic approaches. Even more the consideration of temporal and spatial resolutions differ. This again hampers a generic representation of process models. Third, the automatic identification of treatment configurations may either be achieved by the use of design rules or by permutation of all possible combinations of units stored within a database of treatment units. The first approach depends on past experience translated into design rules. Hence, no innovative new treatment configurations can be identified. The second approach to identify all possible configurations collapses by extremely high numbers of treatment configurations that cannot be mastered. This is due to the phenomena of combinatorial explosion. It follows therefrom that an appropriate planning algorithm should function without the need of additional design rules and should be able to identify directly feasible configurations while discarding those impractical. This work presents a planning tool for the identification and evaluation of treatment configurations that tackles the before addressed problems. The planning tool comprises two major parts. An external declarative knowledge base and the actual planning tool that includes a goal oriented planning algorithm. The knowledge base describes parameters for wastewater characterization (i.e. material model) and a set of treatment units represented by process models (i.e. process model). The formalization of the knowledge base is achieved by the Web Ontology Language (OWL). The developed data model being the organization structure of the knowledge base describes relations between wastewater parameters and process models to enable for generic representation of process models. Through these parameters for wastewater characterization as well as treatment units can be altered or added to the knowledge base without the requirement to synchronize already included parameter representations or process models. Furthermore the knowledge base describes relations between parameters and properties of water constituents. This allows to track changes of all wastewater parameters which result from modeling of removal efficiency of applied treatment units. So far two generic treatment units have been represented within the knowledge base. These are separation and conversion units. These two raw types have been applied to represent different types of clarifiers and biological treatment units. The developed planning algorithm is based on a Means-Ends Analysis (MEA). This is a goal oriented search algorithm that posts goals from wastewater state and limit value restrictions to select those treatment units only that are likely to solve the treatment problem. Regarding this, all treatment units are qualified according to postconditions that describe the effect of each unit. In addition, units are also characterized by preconditions that state the application range of each unit. The developed planning algorithm furthermore allows for the identification of simple cycles to account for moving bed reactor systems (e.g. functional unit of aeration tank and clarifier). The evaluation of identified treatment configurations is achieved by total estimated cost of each configuration. The planning tool has been tested on five use cases. Some use cases contained multiple sources and sinks. This showed the possibility to identify water reuse capabilities as well as to identify solutions that go beyond end of pipe solutions. Beyond the originated area of application, the planning tool may be used for advanced interrogations. Thereby the knowledge base and planning algorithm may be further developed to address the objectives to identify configurations for any type of material and energy recovery

Conceitos e métodos para apoio ao desenvolvimento e avaliação de colaboração remota utilizando realidade aumentada

Remote Collaboration using Augmented Reality (AR) shows great potential to establish a common ground in physically distributed scenarios where team-members need to achieve a shared goal. However, most research efforts in this field have been devoted to experiment with the enabling technology and propose methods to support its development. As the field evolves, evaluation and characterization of the collaborative process become an essential, but difficult endeavor, to better understand the contributions of AR. In this thesis, we conducted a critical analysis to identify the main limitations and opportunities of the field, while situating its maturity and proposing a roadmap of important research actions. Next, a human-centered design methodology was adopted, involving industrial partners to probe how AR could support their needs during remote maintenance. These outcomes were combined with literature methods into an AR-prototype and its evaluation was performed through a user study. From this, it became clear the necessity to perform a deep reflection in order to better understand the dimensions that influence and must/should be considered in Collaborative AR. Hence, a conceptual model and a humancentered taxonomy were proposed to foster systematization of perspectives. Based on the model proposed, an evaluation framework for contextualized data gathering and analysis was developed, allowing support the design and performance of distributed evaluations in a more informed and complete manner. To instantiate this vision, the CAPTURE toolkit was created, providing an additional perspective based on selected dimensions of collaboration and pre-defined measurements to obtain “in situ” data about them, which can be analyzed using an integrated visualization dashboard. The toolkit successfully supported evaluations of several team-members during tasks of remote maintenance mediated by AR. Thus, showing its versatility and potential in eliciting a comprehensive characterization of the added value of AR in real-life situations, establishing itself as a generalpurpose solution, potentially applicable to a wider range of collaborative scenarios.Colaboração Remota utilizando Realidade Aumentada (RA) apresenta um enorme potencial para estabelecer um entendimento comum em cenários onde membros de uma equipa fisicamente distribuídos precisam de atingir um objetivo comum. No entanto, a maioria dos esforços de investigação tem-se focado nos aspetos tecnológicos, em fazer experiências e propor métodos para apoiar seu desenvolvimento. À medida que a área evolui, a avaliação e caracterização do processo colaborativo tornam-se um esforço essencial, mas difícil, para compreender as contribuições da RA. Nesta dissertação, realizámos uma análise crítica para identificar as principais limitações e oportunidades da área, ao mesmo tempo em que situámos a sua maturidade e propomos um mapa com direções de investigação importantes. De seguida, foi adotada uma metodologia de Design Centrado no Humano, envolvendo parceiros industriais de forma a compreender como a RA poderia responder às suas necessidades em manutenção remota. Estes resultados foram combinados com métodos da literatura num protótipo de RA e a sua avaliação foi realizada com um caso de estudo. Ficou então clara a necessidade de realizar uma reflexão profunda para melhor compreender as dimensões que influenciam e devem ser consideradas na RA Colaborativa. Foram então propostos um modelo conceptual e uma taxonomia centrada no ser humano para promover a sistematização de perspetivas. Com base no modelo proposto, foi desenvolvido um framework de avaliação para recolha e análise de dados contextualizados, permitindo apoiar o desenho e a realização de avaliações distribuídas de forma mais informada e completa. Para instanciar esta visão, o CAPTURE toolkit foi criado, fornecendo uma perspetiva adicional com base em dimensões de colaboração e medidas predefinidas para obter dados in situ, que podem ser analisados utilizando o painel de visualização integrado. O toolkit permitiu avaliar com sucesso vários colaboradores durante a realização de tarefas de manutenção remota apoiada por RA, permitindo mostrar a sua versatilidade e potencial em obter uma caracterização abrangente do valor acrescentado da RA em situações da vida real. Sendo assim, estabelece-se como uma solução genérica, potencialmente aplicável a uma gama diversificada de cenários colaborativos.Programa Doutoral em Engenharia Informátic

Psychoanalyzing Nature, Dark Ground of Spirit

The ontological paradigms of Schelling and the late Merleau-Ponty bear striking resemblances to Spinoza’s ontology. Both were developed in response to transcendental models of a Cartesian mold, resisting tendencies to exalt the human ego to the neglect or the detriment of the more-than-human world. As such, thinkers with environmental concerns have sought to derive favorable ethical prescriptions on their basis. We begin by discerning a deadlock between two such thinkers: Ted Toadvine and Sean McGrath. With ecological responsibility in mind, both actually resist Spinozist reduction of the human being to the status of a mere mode among modes. But despite having the same general aim, they end up endorsing contrary practical conclusions. Our objective is to pinpoint the reasons behind this deadlock, indicative of two strands of post-Spinozist environmental thought which stand in tension, and to begin to propose an integrative way forward. The ethical weight afforded by Toadvine to the notion of resistance in the work of the late Merleau-Ponty, namely nature’s resistance to harmonizing, unifying pretensions, invites inquiry into two Merleau-Pontean notions he does not address: the barbarian principle, and the proposal to “Do a Psychoanalysis of Nature.” We trace these to their origins in the works of Schelling’s middle period, arguing that the Schellingian location of resistance in Spirit’s dark ground—alternately conceived as primordial Dionysiac madness, bottled-up within the substratum of consciousness—lends to an understanding of the human, and human responsibility, that harbors favorable implications for environmental ethics