From phenotypes to trees of life : a metamodel-driven approach for the integration of taxonomy models

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Several projects aim at gathering together data concerning life around the world, in order to systematize them and produce a big, unified tree of life. Rather than a static single picture of the living world, this kind of tree: (i) is a result of a dynamic interaction among several models produced by biologists for describing life and expressing how life changes and evolves as time goes by, (ii) is not unique, since there are different competing perspectives describing life (morphology, behavior, ecology, genetics etc.) and different methods of reconstructing evolutionary trees. Our work addresses these problems by proposing a 'superimposed metamodel' mechanism, which acts as a modeling skeleton, supporting a unified view and articulation of models/ontologies involved in tasks that start at collecting data from the field towards producing descriptions and evolutionary trees. It enables to externalize specific knowledge as ontologies and to trace the entire rationale from one extreme of the process to the other one. This paper shows practical experiments in which we explore such characteristics as: guiding the expression of evolutionary hypotheses from observational data, going backwards on the provenance path, or evaluating changes of the tree in front of new evidences collected in the field.Several projects aim at gathering together data concerning life around the world, in order to systematize them and produce a big, unified tree of life. Rather than a static single picture of the living world, this kind of tree: (i) is a result of a dynami16572FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)sem informaçãosem informaçãoIEEE 10th. International conference on e-scienc

Challenges of the Anthropocene epoch – supporting multi-focus research

International audienceWork on multiscale issues presents countless challenges that have been long attacked by GIScience researchers. Most results either concentrate on modeling or on data structures/database aspects. Solutions go either towards generalization (and/or virtualization of distinct scales) or towards linking entities of interest across scales. However, researchers seldom take into account the fact that multiscale scenarios are increasingly constructed cooperatively, and require distinct perspectives of the world. The combination of multiscale and multiple perspectives per scale constitutes what we call multifocus research. This paper presents our solution to these issues. It builds upon a specific database version model – the multiversion MVBD – which has already been successfully implemented in several geospatial scenarios, being extended here to support multi-focus research

Unificando a comparação e busca de fenotipos em model organism databases

[No abstract available]Model Organism Databases (MODs) são largamente utilizados empesquisas nas áreas médica e biológica. Como cada MOD é usualmente especializado em um tipo de organismo - e.g., peixe-zebra, rato, humano, camundongo - torna-se difícil a busca da mesma caracter1442FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2013/08293-7sem informaçãoProceedings of the Brazilian seminar on ontologies (ONTOBRAS

Topical Alignment in Online Social Systems

Understanding the dynamics of social interactions is crucial to comprehend human behavior. The emergence of online social media has enabled access to data regarding people relationships at a large scale. Twitter, specifically, is an information oriented network, with users sharing and consuming information. In this work, we study whether users tend to be in contact with people interested in similar topics, i.e., if they are topically aligned. To do so, we propose an approach based on the use of hashtags to extract information topics from Twitter messages and model users' interests. Our results show that, on average, users are connected with other users similar to them. Furthermore, we show that topical alignment provides interesting information that can eventually allow inferring users' connectivity. Our work, besides providing a way to assess the topical similarity of users, quantifies topical alignment among individuals, contributing to a better understanding of how complex social systems are structured

Fluid Web and digital content components : from the document-centric view to the content-centric view

Orientador: Claudia Bauer MedeirosTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: A Web está evoluindo de um espaço para publicação/consumo de documentos para um ambiente para trabalho colaborativo, onde o conteúdo digital pode viajar e ser replicado, adaptado, decomposto, fundido e transformado. Designamos esta perspectiva por Fluid Web. Esta visão requer uma reformulação geral da abordagem típica orientada a docu­mentos que permeia o gerenciamento de conteúdo na Web. Esta tese apresenta nossa solução para a Fluid Web, que permite nos deslocarmos de uma perspectiva orientada a documentos para outra orientada a conteúdo, onde "conteúdo" pode ser qualquer objeto digital. A solução é baseada em dois eixos: (i) uma unidade auto-descritiva que encap­sula qualquer tipo de artefato de conteúdo - o Componente de Conteúdo Digital (Digital Content Component - DCC); e (ii) uma infraestrutura para a Fluid Web que permite o gerenciamento e distribuição de DCCs na Web, cujo objetivo é dar suporte à colaboração na Web. Concebidos para serem reusados e adaptados, os DCCs encapsulam dados e software usando uma única estrutura, permitindo deste modo composição homogênea e proces­samento de qualquer conteúdo digital, seja este executável ou não. Estas propriedades são exploradas pela nossa infraestrutura para a Fluid Web, que engloba mecanismos de descoberta e de anotação de DCCs em múltiplos níveis, gerenciamento de configurações e controle de versões. Nosso trabalho explora padrões de Web Semântica e ontologias ta­xonômicas, que servem como uma ponte semântica, unificando vocabulários para gerenci­amento de DCCs e facilitando as tarefas de descrição/indexação/descoberta de conteúdo. Os DCCs e sua infraestrura foram implementados e são ilustrados por meio de exemplos práticos, para aplicações científicas. As principais contribuições desta tese são: o modelo de Digital Content Component; o projeto da infraestrutura para a Fluid Web baseada em DCCs, com suporte para armaze­namento baseado em repositórios, compartilhamento, controle de versões e gerenciamento de configurações distribuídas; um algoritmo para a descoberta de conteúdo digital que explora a semântica associada aos DCCs; e a validação prática dos principais conceitos desta pesquisa, com a implementação de protótiposAbstract: The Web is evolving from a space for publicationj consumption of documents to an en­vironment for collaborative work, where digital content can traveI and be replicated, adapted, decomposed, fusioned and transformed. We call this the Fluid Web perspective. This view requires a thorough revision of the typical document-oriented approach that permeates content management on the Web. This thesis presents our solution for the Fluid Web, which allows moving from the document-oriented to a content-oriented pers­pective, where "content" can be any digital object. The solution is based on two axes: a self-descriptive unit to encapsulate any kind of content artifact - the Digital Content Component (DCC); and a Fluid Web infrastructure that provides management and de­ployment of DCCs through the Web, and whose goal is to support collaboration on the Web. Designed to be reused and adapted, DCCs encapsulate data and software using a single structure, thus allowing homogeneous composition and processing of any digital content, be it executable or noto These properties are exploited by our Fluid Web infrastructure, which supports DCC multilevel annotation and discovery mechanisms, configuration ma­nagement and version controI. Our work extensively explores Semantic Web standards and taxonomic ontologies, which serve as a semantic bridge, unifying DCC management vo­cabularies and improving DCC descriptionjindexingjdiscovery. DCCs and infrastructure have been implemented and are illustrated by means of examples, for scientific applicati­ons. The main contributions of this thesis are: the model of Digital Content Component; the design of the Fluid Web infrastructure based on DCCs, with support for repository­based storage, distributed sharing, version control and configuration management; an algorithm for digital content discovery that explores DCe semantics; and a practical validation of the main concepts in this research through implementation of prototypesDoutoradoBanco de DadosMestre em Ciência da Computaçã

Visualização Tridimensional de Dados Espaciais em Ambientes Distribuídos Baseados no Web

This paper discusses how the apllication of existing technology for representing 3D informafion on virtual reality and for managing structured documents can be useful to the development of Web­based Geographic Information Systems. It is presented a generic and extensible solution, based on Resource Description Framework ­ RDF, for the introduction of meaning to the elements of the Virtual Modeling Language ­ VRML. The paper also presents an extensible an highly interactive for Geographic Information Systems, based on such solution

Self Describing Components: Searching for Digital Artifacts on the Web

Abstract. The Semantic Web has opened new horizons in exploring Web functionality. One of the many challenges is to proactively support the reuse of digital artifacts stored in repositories all over the world. Our goal is to contribute towards this issue, proposing a mechanism for describing and discovering artifacts called Digital Content Components (DCCs). DCCs are self-contained stored entities that may comprise any digital content, such as pieces of software, multimedia or text. Their specification takes advantage of Semantic Web standards and ontologies, both of which are used in the discovery process. DCC construction and composition procedures naturally lend themselves to patternmatching and subsumption-based search. Thus, many existing methods for Web searching can be extended to look for reusable artifacts. We validate the proposal discussing its implementation for agro-environmental planning.

Geographic digital content components

Projects using geographic information tools involve a large variety of data objects, represented in different formats. Many efforts pursue standards to represent each kind of data object, and the interoperability between geographic information tools. The proliferation of data and tools raises the need for their reuse. This need can be extended to project reuse. This work presents a proposal to reuse geographic information projects based on a model called digital content component. This model can represent all elements involved in a project - including software components - and their relationship in a open homogeneous format.Pages: 281-29

Web metalaboratory : composition of laboratories on the web

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)The amount of scientific data, services and on-line tools available on the Web offers an unprecedented opportunity to conceive new kinds of laboratories able to blend these resources. Existing experimental and collected data can substantiate asynchronous laboratories. Combined with mashup enabled software, it is possible to produce hybrid laboratories to confront, for example, synthetic simulations with observations. This work addresses this opportunity in the Education context through our metalaboratory, an authoring tool to produce laboratories by combining building blocks encapsulated in components. It introduces lab composition patterns and active Web templates as fundamental mechanisms to support a lab authoring task. Laboratories can be embedded and 'mashed-up' in Web documents. The paper shows practical experiments of producing Web virtual and hybrid laboratories.The amount of scientific data, services and on-line tools available on the Web offers an unprecedented opportunity to conceive new kinds of laboratories able to blend these resources. Existing experimental and collected data can substantiate asynchronous24348FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)sem informaçãosem informaçãoIEEE 10th. International conference on e-Scienc