In silico scientific experiments encompass multiple combinations of program and data resources. E... more In silico scientific experiments encompass multiple combinations of program and data resources. Each resource combination in an execution flow is called a scientific workflow. In bioinformatics environments, program composition is a frequent operation, requiring complex management. A scientist faces many challenges when building an experiment: finding the right program to use, the adequate parameters to tune, managing input/output data, building and reusing workflows. Typically, these workflows are implemented using script languages because of their simplicity, despite their specificity and difficulty of reuse. In contrast, Web service technology was specially conceived to encapsulate and combine programs and data, providing interoperation between applications from different platforms. The Web services approach is superior to scripts with regard to interoperability, scalability and flexibility issues. We have combined metadata support with Web services within a framework that supports scientific workflows. While most works are focused on metadata issues to manage and integrate heterogeneous scientific data sources, in this work we concentrate on metadata support to program management within workflows. We have used this framework with a real structural genomic workflow, showing its viability and evidencing its advantages.
Ranganathan, an Indian mathematician and librarian, has proposed a set of comprehensible canons t... more Ranganathan, an Indian mathematician and librarian, has proposed a set of comprehensible canons to provide guidance to the process of building concept hierarchies. It is our proposition that Ranganathans canons can contribute to fulfill the gap between the high-level domain conceptualization guided by top level ontologies and the classification of such concepts within facets, needed when building ontologies taxonomical structures. In order to show the utility of Ranganathans canons applied to ontology structuring, we have analyzed the structure of a biomedical ontology: Gene Ontology (GO). As result, we have found that many of the existing inconsistencies on GO hierarchies could be avoided if Ranganathans canons were adopted.
Proceedings of the 2011 15th International Conference on Computer Supported Cooperative Work in Design (CSCWD), 2011
The evolution of communication channels and social networks proliferation through the web are ins... more The evolution of communication channels and social networks proliferation through the web are inspiring and enabling the construction of collaborative environments. This article proposes an architecture of processes that aims to identify information responsibilities within a general emergency scenario, considering a new way of data provenance: citizens and government agencies. Citizens, who experience as victims a chaotic scenario, can also act as collaborators, providing relevant and useful information for the decision-making process. Today, they already do this informally, sharing public interest information through social networks, such as the Tweeter. The architecture also provides procedures for treating reliability and credibility of the information, provided by the so-called "anonymous officials", subjecting it to a filtering and verification process. The heterogeneity of information formats is a wellknown problem that affects organizations and communities that wants to access public data. The architecture includes a Linked Open Data (LOD) approach for acquisition and integration of data maintained by government agencies that adopt different publishing standards. A solution to this problem is of particular importance to emergency response organizations that need access to all information available to better respond to disasters and crisis.
Abstract. Provenance is a term used to describe the history, lineage or origins of a piece of dat... more Abstract. Provenance is a term used to describe the history, lineage or origins of a piece of data. In scientific experiments that are computationally intensive the data resources are produced in large-scale. Thus, as more scientific data are produced the importance of tracking and sharing its metadata grows. Therefore, it is desirable to make it easy to access, share, reuse, integrate and reason. To address these requirements ontologies can be of use to encode expectations and agreements concerning provenance metadata reuse and integration. In this paper, we present a well-founded provenance ontology named Open proVenance Ontology (OvO) which takes inspiration on three theories: the lifecycle of in silico scientific experiments, the Open Provenance Model (OPM) and the Unified Foundational Ontology (UFO). OvO may act as a reference conceptual model that can be used by researchers to explore the semantics of provenance metadata. 1.
Nos últimos anos tem havido um impulso no número de ontologias produzidas, refletindo um contínuo... more Nos últimos anos tem havido um impulso no número de ontologias produzidas, refletindo um contínuo amadurecimento dos esforços de desenvolvimento de vocabulários, em especial na área de Biomedicina, caracterizada como um domínio inter e multidisciplinar e de temática complexa. Entretanto, apesar de haver propostas metodológicas e de melhores práticas sobre como organizar a estrutura terminológica de ontologias e de suas relações, pouco se explica sobre os métodos adotados para o levantamento terminológico do seu domínio e da delimitação de seu escopo, especialmente considerando o reuso de ontologias. O objetivo desse trabalho é apresentar as bases da Ciência da Informação e da Computação para atividades de reuso em ontologias, como um passo metodológico para a aquisição de conhecimento, visando possibilitar mecanismos para o mapeamento e alinhamento de termos em ontologias no domínio dos Tripanosomatídeos.
MiddLog is an extensible and configurable logging infrastructure based on the middleware technolo... more MiddLog is an extensible and configurable logging infrastructure based on the middleware technology. It includes a set of classes and components that are deployed on an application server, performing analysis and recordings of application events at a log file, in a dynamic and transparent way. MiddLog's extension capability enables its users to increase its services by aggregating new features or creating new components and inserting them into the infrastructure. This paper focuses on three major parts of MiddLog: interception layer, integration layer and processing messages layer.
During the last 30 years, decisions involving conventional data have been supported by traditiona... more During the last 30 years, decisions involving conventional data have been supported by traditional decision support systems, like EIS (Executive Information Systems), DSS (Decision Support Systems) and lately OLAP (On-Line Analytical Processing) systems on Data Warehouse ( ...
With the growth of e-government programs, the available data to citizens is growing in volume eve... more With the growth of e-government programs, the available data to citizens is growing in volume every day. However, to make these data a useful source of information, to be referenced and integrated more easily by different applications, they should be published according to the best practices of Linked Open Data, using standards for description (RDF) and identification (URI) of data resources on the web. The main goal of this work is to propose a platform and approach to support the exposure, sharing and association of data resources in the form of Linked Open Data, offering a user-friendly environment to stimulate the publication of data and their association to other existing data. Central functionalities to be included are data cleaning, transformation, linking, annotation and referencing to terminology mechanisms.
Mara Abel, Federal University of Rio Grande do Sul, Brazil Colin Atkinson, University of Mannheim... more Mara Abel, Federal University of Rio Grande do Sul, Brazil Colin Atkinson, University of Mannheim, Germany Ebrahim Bagheri, National Research Council of Canada, Canada Luiz Olavo Bonino da Silva Santos, University of Twente, The Netherlands Christoph Bussler, Merced Systems, Inc., USA Maria Luiza Campos, Federal University of Rio de Janeiro, Brazil Oscar Corcho, Universidad Politécnica de Madrid, Spain Jens Dietrich, Massey University, New Zealand Vadim Ermolayev, Zaporozhye National University, Ukraine Joerg Evermann, Memorial ...
With the growth of e-government programs, the available data to citizens is growing in volume eve... more With the growth of e-government programs, the available data to citizens is growing in volume every day. However, to make these data a useful source of information, to be referenced and integrated more easily by different applications, they should be published according to the best practices of Linked Open Data, using standards for description (RDF) and identification (URI) of data resources on the web. The main goal of this work is to propose a platform and approach to support the exposure, sharing and association of data resources in the form of Linked Open Data, offering a user-friendly environment to stimulate the publication of data and their association to other existing data. Central functionalities to be included are data cleaning, transformation, linking, annotation and referencing to terminology mechanisms.
In silico scientific experiments encompass multiple combinations of program and data resources. E... more In silico scientific experiments encompass multiple combinations of program and data resources. Each resource combination in an execution flow is called a scientific workflow. In bioinformatics environments, program composition is a frequent operation, requiring complex management. A scientist faces many challenges when building an experiment: finding the right program to use, the adequate parameters to tune, managing input/output data, building and reusing workflows. Typically, these workflows are implemented using script languages because of their simplicity, despite their specificity and difficulty of reuse. In contrast, Web service technology was specially conceived to encapsulate and combine programs and data, providing interoperation between applications from different platforms. The Web services approach is superior to scripts with regard to interoperability, scalability and flexibility issues. We have combined metadata support with Web services within a framework that supports scientific workflows. While most works are focused on metadata issues to manage and integrate heterogeneous scientific data sources, in this work we concentrate on metadata support to program management within workflows. We have used this framework with a real structural genomic workflow, showing its viability and evidencing its advantages.
Ranganathan, an Indian mathematician and librarian, has proposed a set of comprehensible canons t... more Ranganathan, an Indian mathematician and librarian, has proposed a set of comprehensible canons to provide guidance to the process of building concept hierarchies. It is our proposition that Ranganathans canons can contribute to fulfill the gap between the high-level domain conceptualization guided by top level ontologies and the classification of such concepts within facets, needed when building ontologies taxonomical structures. In order to show the utility of Ranganathans canons applied to ontology structuring, we have analyzed the structure of a biomedical ontology: Gene Ontology (GO). As result, we have found that many of the existing inconsistencies on GO hierarchies could be avoided if Ranganathans canons were adopted.
Proceedings of the 2011 15th International Conference on Computer Supported Cooperative Work in Design (CSCWD), 2011
The evolution of communication channels and social networks proliferation through the web are ins... more The evolution of communication channels and social networks proliferation through the web are inspiring and enabling the construction of collaborative environments. This article proposes an architecture of processes that aims to identify information responsibilities within a general emergency scenario, considering a new way of data provenance: citizens and government agencies. Citizens, who experience as victims a chaotic scenario, can also act as collaborators, providing relevant and useful information for the decision-making process. Today, they already do this informally, sharing public interest information through social networks, such as the Tweeter. The architecture also provides procedures for treating reliability and credibility of the information, provided by the so-called "anonymous officials", subjecting it to a filtering and verification process. The heterogeneity of information formats is a wellknown problem that affects organizations and communities that wants to access public data. The architecture includes a Linked Open Data (LOD) approach for acquisition and integration of data maintained by government agencies that adopt different publishing standards. A solution to this problem is of particular importance to emergency response organizations that need access to all information available to better respond to disasters and crisis.
Abstract. Provenance is a term used to describe the history, lineage or origins of a piece of dat... more Abstract. Provenance is a term used to describe the history, lineage or origins of a piece of data. In scientific experiments that are computationally intensive the data resources are produced in large-scale. Thus, as more scientific data are produced the importance of tracking and sharing its metadata grows. Therefore, it is desirable to make it easy to access, share, reuse, integrate and reason. To address these requirements ontologies can be of use to encode expectations and agreements concerning provenance metadata reuse and integration. In this paper, we present a well-founded provenance ontology named Open proVenance Ontology (OvO) which takes inspiration on three theories: the lifecycle of in silico scientific experiments, the Open Provenance Model (OPM) and the Unified Foundational Ontology (UFO). OvO may act as a reference conceptual model that can be used by researchers to explore the semantics of provenance metadata. 1.
Nos últimos anos tem havido um impulso no número de ontologias produzidas, refletindo um contínuo... more Nos últimos anos tem havido um impulso no número de ontologias produzidas, refletindo um contínuo amadurecimento dos esforços de desenvolvimento de vocabulários, em especial na área de Biomedicina, caracterizada como um domínio inter e multidisciplinar e de temática complexa. Entretanto, apesar de haver propostas metodológicas e de melhores práticas sobre como organizar a estrutura terminológica de ontologias e de suas relações, pouco se explica sobre os métodos adotados para o levantamento terminológico do seu domínio e da delimitação de seu escopo, especialmente considerando o reuso de ontologias. O objetivo desse trabalho é apresentar as bases da Ciência da Informação e da Computação para atividades de reuso em ontologias, como um passo metodológico para a aquisição de conhecimento, visando possibilitar mecanismos para o mapeamento e alinhamento de termos em ontologias no domínio dos Tripanosomatídeos.
MiddLog is an extensible and configurable logging infrastructure based on the middleware technolo... more MiddLog is an extensible and configurable logging infrastructure based on the middleware technology. It includes a set of classes and components that are deployed on an application server, performing analysis and recordings of application events at a log file, in a dynamic and transparent way. MiddLog's extension capability enables its users to increase its services by aggregating new features or creating new components and inserting them into the infrastructure. This paper focuses on three major parts of MiddLog: interception layer, integration layer and processing messages layer.
During the last 30 years, decisions involving conventional data have been supported by traditiona... more During the last 30 years, decisions involving conventional data have been supported by traditional decision support systems, like EIS (Executive Information Systems), DSS (Decision Support Systems) and lately OLAP (On-Line Analytical Processing) systems on Data Warehouse ( ...
With the growth of e-government programs, the available data to citizens is growing in volume eve... more With the growth of e-government programs, the available data to citizens is growing in volume every day. However, to make these data a useful source of information, to be referenced and integrated more easily by different applications, they should be published according to the best practices of Linked Open Data, using standards for description (RDF) and identification (URI) of data resources on the web. The main goal of this work is to propose a platform and approach to support the exposure, sharing and association of data resources in the form of Linked Open Data, offering a user-friendly environment to stimulate the publication of data and their association to other existing data. Central functionalities to be included are data cleaning, transformation, linking, annotation and referencing to terminology mechanisms.
Mara Abel, Federal University of Rio Grande do Sul, Brazil Colin Atkinson, University of Mannheim... more Mara Abel, Federal University of Rio Grande do Sul, Brazil Colin Atkinson, University of Mannheim, Germany Ebrahim Bagheri, National Research Council of Canada, Canada Luiz Olavo Bonino da Silva Santos, University of Twente, The Netherlands Christoph Bussler, Merced Systems, Inc., USA Maria Luiza Campos, Federal University of Rio de Janeiro, Brazil Oscar Corcho, Universidad Politécnica de Madrid, Spain Jens Dietrich, Massey University, New Zealand Vadim Ermolayev, Zaporozhye National University, Ukraine Joerg Evermann, Memorial ...
With the growth of e-government programs, the available data to citizens is growing in volume eve... more With the growth of e-government programs, the available data to citizens is growing in volume every day. However, to make these data a useful source of information, to be referenced and integrated more easily by different applications, they should be published according to the best practices of Linked Open Data, using standards for description (RDF) and identification (URI) of data resources on the web. The main goal of this work is to propose a platform and approach to support the exposure, sharing and association of data resources in the form of Linked Open Data, offering a user-friendly environment to stimulate the publication of data and their association to other existing data. Central functionalities to be included are data cleaning, transformation, linking, annotation and referencing to terminology mechanisms.
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Papers by Maria Luiza