Journals and repositories: an evolving relationship?

It is now widely accepted that there are two routes to open access (OA): OA repositories and OA journals. It is often assumed these are distinct alternative parallel tracks. However, it has recently become clear that there is potential for repositories and journals to interact with each other on an ongoing basis and between them to form a coherent OA scholarly communication system. This paper puts forward three possible models of interaction between repositories and journals; services such as arXiv and PubMed Central, and the work carried out by the RIOJA project, are working exemplars and pilot implementations of these models. The key issues associated with the widespread adoption of these models include repository infrastructure development; changing ideas of the ‘journal’, ‘article’, and ‘publication’; version management; quality assurance; business and funding models; developing value-added features; content preservation; policy frameworks; and changing roles and cultures within the research community.

Students' collective knowledge construction in the virtual learning environment ""ToLigado - your school interactive newspaper""

Introduction. The ToLigado Project - Your School Interactive Newspaper is an interactive virtual learning environment conceived, developed, implemented and supported by researchers at the School of the Future Research Laboratory of the University of Sao Paulo, Brazil. Method. This virtual learning environment aims to motivate trans-disciplinary research among public school students and teachers in 2,931 schools equipped with Internet-access computer rooms. Within this virtual community, students produce collective multimedia research documents that are immediately published in the portal. The project also aims to increase students' autonomy for research, collaborative work and Web authorship. Main sections of the portal are presented and described. Results. Partial results of the first two years' implementation are presented and indicate a strong motivation among students to produce knowledge despite the fragile hardware and software infrastructure at the time. Discussion. In this new environment, students should be seen as 'knowledge architects' and teachers as facilitators, or 'curiosity managers'. The ToLigado portal may constitute a repository for future studies regarding student attitudes in virtual learning environments, students' behaviour as 'authors', Web authorship involving collective knowledge production, teachers' behaviour as facilitators, and virtual learning environments as digital repositories of students' knowledge construction and social capital in virtual learning communities.

The Use of Latent Semantic Indexing to Mitigate OCR Effects of Related Document Images

Due to both the widespread and multipurpose use of document images and the current availability of a high number of document images repositories, robust information retrieval mechanisms and systems have been increasingly demanded. This paper presents an approach to support the automatic generation of relationships among document images by exploiting Latent Semantic Indexing (LSI) and Optical Character Recognition (OCR). We developed the LinkDI (Linking of Document Images) service, which extracts and indexes document images content, computes its latent semantics, and defines relationships among images as hyperlinks. LinkDI was experimented with document images repositories, and its performance was evaluated by comparing the quality of the relationships created among textual documents as well as among their respective document images. Considering those same document images, we ran further experiments in order to compare the performance of LinkDI when it exploits or not the LSI technique. Experimental results showed that LSI can mitigate the effects of usual OCR misrecognition, which reinforces the feasibility of LinkDI relating OCR output with high degradation.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Learning about knowledge management for improving environmental impact assessment in a government agency: The Western Australian experience

How does knowledge management (KM) by a government agency responsible for environmental impact assessment (EIA) potentially contribute to better environmental assessment and management practice? Staff members at government agencies in charge of the EIA process are knowledge workers who perform judgement-oriented tasks highly reliant on individual expertise, but also grounded on the agency`s knowledge accumulated over the years. Part of an agency`s knowledge can be codified and stored in an organizational memory, but is subject to decay or loss if not properly managed. The EIA agency operating in Western Australia was used as a case study. Its KM initiatives were reviewed, knowledge repositories were identified and staff surveyed to gauge the utilisation and effectiveness of such repositories in enabling them to perform EIA tasks. Key elements of KM are the preparation of substantive guidance and spatial information management. It was found that treatment of cumulative impacts on the environment is very limited and information derived from project follow-up is not properly captured and stored, thus not used to create new knowledge and to improve practice and effectiveness. Other opportunities for improving organizational learning include the use of after-action reviews. The learning about knowledge management in EIA practice gained from Western Australian experience should be of value to agencies worldwide seeking to understand where best to direct their resources for their own knowledge repositories and environmental management practice. (C) 2011 Elsevier Ltd. All rights reserved.

Making Fedora easier to implement with Fez: A free open source content model and workflow management front-end to Fedora

The University of Queensland, Australia has developed Fez, a world-leading user-interface and management system for Fedora-based institutional repositories, which bridges the gap between a repository and users. Christiaan Kortekaas, Andrew Bennett and Keith Webster will review this open source software that gives institutions the power to create a comprehensive repository solution without the hassle..

Migrating eprints.org data to a Fez repository

This document records the process of migrating eprints.org data to a Fez repository. Fez is a Web-based digital repository and workflow management system based on Fedora (http://www.fedora.info/). At the time of migration, the University of Queensland Library was using EPrints 2.2.1 [pepper] for its ePrintsUQ repository. Once we began to develop Fez, we did not upgrade to later versions of eprints.org software since we knew we would be migrating data from ePrintsUQ to the Fez-based UQ eSpace. Since this document records our experiences of migration from an earlier version of eprints.org, anyone seeking to migrate eprints.org data into a Fez repository might encounter some small differences. Moving UQ publication data from an eprints.org repository into a Fez repository (hereafter called UQ eSpace (http://espace.uq.edu.au/) was part of a plan to integrate metadata (and, in some cases, full texts) about all UQ research outputs, including theses, images, multimedia and datasets, in a single repository. This tied in with the plan to identify and capture the research output of a single institution, the main task of the eScholarshipUQ testbed for the Australian Partnership for Sustainable Repositories project (http://www.apsr.edu.au/). The migration could not occur at UQ until the functionality in Fez was at least equal to that of the existing ePrintsUQ repository. Accordingly, as Fez development occurred throughout 2006, a list of eprints.org functionality not currently supported in Fez was created so that programming of such development could be planned for and implemented.

Impact of Commercial Search Engines and International Databases on Engineering Teaching and Research

For the last three decades, the engineering higher education and professional environments have been completely transformed by the "electronic/digital information revolution" that has included the introduction of personal computer, the development of email and world wide web, and broadband Internet connections at home. Herein the writer compares the performances of several digital tools with traditional library resources. While new specialised search engines and open access digital repositories may fill a gap between conventional search engines and traditional references, these should be not be confused with real libraries and international scientific databases that encompass textbooks and peer-reviewed scholarly works. An absence of listing in some Internet search listings, databases and repositories is not an indication of standing. Researchers, engineers and academics should remember these key differences in assessing the quality of bibliographic "research" based solely upon Internet searches.

e-learning in the classroom?

As teachers, we are challenged everyday to solve pedagogical problems and we have to fight for our students’ attention in a media rich world. I will talk about how we use ICT in Initial Teacher Training and give you some insight on what we are doing. The most important benefit of using ICT in education is that it makes us reflect on our practice. There is no doubt that our classrooms need to be updated, but we need to be critical about every peace of hardware, software or service that we bring into them. It is not only because our budgets are short, but also because e‐learning is primarily about learning, not technology. Therefore, we need to have the knowledge and skills required to act in different situations, and choose the best tool for the job. Not all subjects are suitable for e‐learning, nor do all students have the skills to organize themselves their own study times. Also not all teachers want to spend time programming or learning about instructional design and metadata. The promised land of easy use of authoring tools (e.g. eXe and Reload) that will lead to all teachers become Learning Objects authors and share these LO in Repositories, all this failed, like previously HyperCard, Toolbook and others. We need to know a little bit of many different technologies so we can mobilize this knowledge when a situation requires it: integrate e‐learning technologies in the classroom, not a flipped classroom, just simple tools. Lecture capture, mobile phones and smartphones, pocket size camcorders, VoIP, VLE, live video broadcast, screen sharing, free services for collaborative work, save, share and sync your files. Do not feel stressed to use everything, every time. Just because we have a whiteboard does not mean we have to make it the centre of the classroom. Start from where you are, with your preferred subject and the tools you master. Them go slowly and try some new tool in a non‐formal situation and with just one or two students. And you don’t need to be alone: subscribe a mailing list and share your thoughts with other teachers in a dedicated forum, even better if both are part of a community of practice, and share resources. We did that for music teachers and it was a success, in two years arriving at 1.000 members. Just do it.

Que learning objects (LOs) utilizam as instituições de ensino superior ?

O uso das tecnologias com base na Web, no processo ensino/aprendizagem, têm obtido excelentes resultados, onde a Internet é a plataforma base de comunicação e interacção entre estudantes e professores. Assiste-se, também, a uma partilha/reutilização constante de conteúdos educativos/Learning Objects, em diferentes formatos e diferentes tipos de plataformas, incrementada pela Web 2.0. Este artigo apresenta um estudo sobre o desenvolvimento, disponibilização e utilização de Learning Objects em instituições de Ensino Superior. Conclui-se que as instituições de Ensino Superior inquiridas não desenvolvem, não reutilizam nem promovem a reutilização de LOs, que utilizam as especificações SCORM e IMS, e apresentam-se observações sobre as vantagens e desvantagens da sua utilização.

Ontologies for reusing data cleaning knowledge

The emergence of new business models, namely, the establishment of partnerships between organizations, the chance that companies have of adding existing data on the web, especially in the semantic web, to their information, led to the emphasis on some problems existing in databases, particularly related to data quality. Poor data can result in loss of competitiveness of the organizations holding these data, and may even lead to their disappearance, since many of their decision-making processes are based on these data. For this reason, data cleaning is essential. Current approaches to solve these problems are closely linked to database schemas and specific domains. In order that data cleaning can be used in different repositories, it is necessary for computer systems to understand these data, i.e., an associated semantic is needed. The solution presented in this paper includes the use of ontologies: (i) for the specification of data cleaning operations and, (ii) as a way of solving the semantic heterogeneity problems of data stored in different sources. With data cleaning operations defined at a conceptual level and existing mappings between domain ontologies and an ontology that results from a database, they may be instantiated and proposed to the expert/specialist to be executed over that database, thus enabling their interoperability.

Indexação e pesquisa de informação com base em ontologias interligadas

Tecnologias da Web Semântica como RDF, OWL e SPARQL sofreram nos últimos anos um forte crescimento e aceitação. Projectos como a DBPedia e Open Street Map começam a evidenciar o verdadeiro potencial da Linked Open Data. No entanto os motores de pesquisa semânticos ainda estão atrasados neste crescendo de tecnologias semânticas. As soluções disponíveis baseiam-se mais em recursos de processamento de linguagem natural. Ferramentas poderosas da Web Semântica como ontologias, motores de inferência e linguagens de pesquisa semântica não são ainda comuns. Adicionalmente a esta realidade, existem certas dificuldades na implementação de um Motor de Pesquisa Semântico. Conforme demonstrado nesta dissertação, é necessária uma arquitectura federada de forma a aproveitar todo o potencial da Linked Open Data. No entanto um sistema federado nesse ambiente apresenta problemas de performance que devem ser resolvidos através de cooperação entre fontes de dados. O standard actual de linguagem de pesquisa na Web Semântica, o SPARQL, não oferece um mecanismo para cooperação entre fontes de dados. Esta dissertação propõe uma arquitectura federada que contém mecanismos que permitem cooperação entre fontes de dados. Aborda o problema da performance propondo um índice gerido de forma centralizada assim como mapeamentos entre os modelos de dados de cada fonte de dados. A arquitectura proposta é modular, permitindo um crescimento de repositórios e funcionalidades simples e de forma descentralizada, à semelhança da Linked Open Data e da própria World Wide Web. Esta arquitectura trabalha com pesquisas por termos em linguagem natural e também com inquéritos formais em linguagem SPARQL. No entanto os repositórios considerados contêm apenas dados em formato RDF. Esta dissertação baseia-se em múltiplas ontologias partilhadas e interligadas.

Air pollution from traffic emissions in Oporto, Portugal: health and environmental implications

Air pollution represents a serious risk not only to environment and human health, but also to historical heritage. In this study, air pollution of the Oporto Metropolitan Area and its main impacts were characterized. The results showed that levels of CO, PM10 and SO2 have been continuously decreasing in the respective metropolitan area while levels of NOx and NO2 have not changed significantly. Traffic emissions were the main source of the determined polycyclic aromatic hydrocarbons (PAHs; 16 PAHs considered by U.S. EPA as priority pollutants, dibenzo[a,l]pyrene and benzo[j]fluoranthene) in air of the respective metropolitan area. The mean concentration of 18 PAHs in air was 69.9±39.7 ng m−3 with 3–4 rings PAHs accounting for 75% of the total ΣPAHs. The health risk analysis of PAHs in air showed that the estimated values of lifetime lung cancer risks considerably exceeded the health-based guideline level. Analytical results also confirm that historical monuments in urban areas act as passive repositories for air pollutants present in the surrounding atmosphere. FTIR and EDX analyses showed that gypsum was the most important constituent of black crusts of the characterized historical monument Monastery of Serra do Pilar classified as “UNESCO World Cultural Heritage”. In black crusts, 4–6 rings compounds accounted approximately for 85% of ΣPAHs. The diagnostic ratios confirmed that traffic emissions were the major source of PAHs in black crusts; PAH composition profiles were very similar for crusts and PM10 and PM2.5.

Evaluation of atmospheric deposition and patterns of polycyclic aromatic hydrocarbons in façades of historic monuments of Oporto (Portugal)

Atmospheric pollution by motor vehicles is considered a relevant source of damage to architectural heritage. Thus the aim of this work was to assess the atmospheric depositions and patterns of polycyclic aromatic hydrocarbons (PAHs) in façades of historical monuments. Eighteen PAHs (16 PAHs considered by US EPA as priority pollutants, dibenzo[a,l]pyrene and benzo[j]fluoranthene) were determined in thin black layers collected from façades of two historical monuments: Hospital Santo António and Lapa Church (Oporto, Portugal). Scanning electron microscopy (SEM) was used for morphological and elemental characterisation of thin black layers; PAHs were quantified by microwave-assisted extraction combined with liquid chromatography (MAE-LC). The thickness of thin black layers were 80–110 μm and they contained significant levels of iron, sulfur, calcium and phosphorus. Total concentrations of 18 PAHs ranged from 7.74 to 147.92 ng/g (mean of 45.52 ng/g) in thin black layers of Hospital Santo António, giving a range three times lower than at Lapa Church (5.44– 429.26 ng/g; mean of 110.25 ng/g); four to six rings compounds accounted at both monuments approximately for 80–85% of ΣPAHs. The diagnostic ratios showed that traffic emissions were significant source of PAHs in thin black layers. Composition profiles of PAHs in thin black layers of both monuments were similar to those of ambient air, thus showing that air pollution has a significant impact on the conditions and stone decay of historical building façades. The obtained results confirm that historical monuments in urban areas act as passive repositories for air pollutants present in the surrounding atmosphere.

BabeLO : an extensible converter of programming exercises formats

In the last two decades, there was a proliferation of programming exercise formats that hinders interoperability in automatic assessment. In the lack of a widely accepted standard, a pragmatic solution is to convert content among the existing formats. BabeLO is a programming exercise converter providing services to a network of heterogeneous e-learning systems such as contest management systems, programming exercise authoring tools, evaluation engines and repositories of learning objects. Its main feature is the use of a pivotal format to achieve greater extensibility. This approach simplifies the extension to other formats, just requiring the conversion to and from the pivotal format. This paper starts with an analysis of programming exercise formats representative of the existing diversity. This analysis sets the context for the proposed approach to exercise conversion and to the description of the pivotal data format. The abstract service definition is the basis for the design of BabeLO, its components and web service interface. This paper includes a report on the use of BabeLO in two concrete scenarios: to relocate exercises to a different repository, and to use an evaluation engine in a network of heterogeneous systems.